Starting phenix.real_space_refine on Mon Mar 11 12:42:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0e_24788/03_2024/7s0e_24788.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0e_24788/03_2024/7s0e_24788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0e_24788/03_2024/7s0e_24788.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0e_24788/03_2024/7s0e_24788.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0e_24788/03_2024/7s0e_24788.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0e_24788/03_2024/7s0e_24788.pdb" } 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 Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 1": "OD1" <-> "OD2" Residue "L ASP 28": "OD1" <-> "OD2" Residue "L ASP 70": "OD1" <-> "OD2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "L PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 122": "OD1" <-> "OD2" Residue "L ASP 170": "OD1" <-> "OD2" Residue "L TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 195": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 8.43, per 1000 atoms: 1.02 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.65 Conformation dependent library (CDL) restraints added in 2.9 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: 1.21 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: 2.78 Time building geometry restraints manager: 4.85 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: 99.88 - 107.06: 271 107.06 - 114.25: 4725 114.25 - 121.43: 4153 121.43 - 128.62: 2315 128.62 - 135.80: 50 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 2.520 nonbonded pdb=" N ALA H 166 " pdb=" O THR H 201 " model vdw 2.090 2.520 nonbonded pdb=" OG1 THR H 28 " pdb=" OG SER H 31 " model vdw 2.133 2.440 nonbonded pdb=" OG SER A 469 " pdb=" OE1 GLU A 471 " model vdw 2.158 2.440 ... (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 ========== 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: 4.450 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: 17.850 Check model and map are aligned: 0.160 Set scattering table: 0.070 Process input model: 33.420 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8449 Z= 0.272 Angle : 0.868 13.225 11514 Z= 0.524 Chirality : 0.053 0.389 1290 Planarity : 0.006 0.085 1490 Dihedral : 13.436 88.828 2954 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.66 % Allowed : 8.06 % Favored : 91.27 % Rotamer: Outliers : 1.22 % Allowed : 0.78 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.25), residues: 1059 helix: -2.63 (0.67), residues: 49 sheet: -0.61 (0.30), residues: 285 loop : -1.35 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP L 91 HIS 0.004 0.001 HIS H 208 PHE 0.023 0.002 PHE A 329 TYR 0.016 0.002 TYR L 49 ARG 0.006 0.001 ARG L 142 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 0.975 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: 0.1804 time to fit residues: 34.1970 Evaluate side-chains 87 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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: 3.9990 chunk 44 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 54 optimal weight: 0.3980 chunk 42 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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 196 ASN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 53 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 8449 Z= 0.309 Angle : 0.754 12.697 11514 Z= 0.404 Chirality : 0.047 0.198 1290 Planarity : 0.006 0.086 1490 Dihedral : 6.334 37.341 1159 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 25.90 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.30 % Favored : 90.32 % Rotamer: Outliers : 0.22 % Allowed : 4.10 % Favored : 95.68 % 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: -2.00 (0.24), residues: 1059 helix: -2.99 (0.53), residues: 54 sheet: -0.91 (0.28), residues: 304 loop : -1.43 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A 353 HIS 0.009 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 H 98 *********************** 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 106 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 374 PHE cc_start: 0.7834 (m-10) cc_final: 0.7524 (m-80) REVERT: A 392 PHE cc_start: 0.7768 (m-80) cc_final: 0.6750 (m-80) REVERT: H 5 VAL cc_start: 0.8908 (m) cc_final: 0.8695 (p) REVERT: H 79 LEU cc_start: 0.9055 (tp) cc_final: 0.8806 (tp) REVERT: H 158 VAL cc_start: 0.7899 (m) cc_final: 0.7602 (p) REVERT: L 4 MET cc_start: 0.8500 (mpp) cc_final: 0.8178 (mpp) REVERT: L 71 PHE cc_start: 0.7626 (m-80) cc_final: 0.6826 (m-80) REVERT: L 175 LEU cc_start: 0.8759 (tp) cc_final: 0.8543 (tp) outliers start: 2 outliers final: 1 residues processed: 106 average time/residue: 0.1737 time to fit residues: 27.1324 Evaluate side-chains 76 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 0.0570 chunk 29 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 85 optimal weight: 0.0470 chunk 95 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 165 ASN A 196 ASN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.2472 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= 0.196 Angle : 0.670 13.755 11514 Z= 0.352 Chirality : 0.046 0.180 1290 Planarity : 0.005 0.055 1490 Dihedral : 5.679 35.967 1159 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.59 % Favored : 92.03 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % 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: -1.82 (0.24), residues: 1059 helix: -2.88 (0.55), residues: 54 sheet: -0.71 (0.28), residues: 300 loop : -1.33 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 353 HIS 0.004 0.001 HIS H 208 PHE 0.020 0.002 PHE A 275 TYR 0.024 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 115 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.7754 (m-80) cc_final: 0.6909 (m-80) REVERT: A 398 ASP cc_start: 0.7989 (m-30) cc_final: 0.7772 (m-30) REVERT: H 5 VAL cc_start: 0.8834 (m) cc_final: 0.8568 (p) REVERT: L 1 ASP cc_start: 0.7851 (m-30) cc_final: 0.7275 (t70) REVERT: L 70 ASP cc_start: 0.8992 (p0) cc_final: 0.8749 (p0) REVERT: L 71 PHE cc_start: 0.7447 (m-80) cc_final: 0.6526 (m-80) REVERT: L 175 LEU cc_start: 0.8923 (tp) cc_final: 0.8630 (tp) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1771 time to fit residues: 29.6626 Evaluate side-chains 73 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 96 optimal weight: 0.3980 chunk 102 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 85 optimal weight: 0.0030 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 196 ASN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 8449 Z= 0.190 Angle : 0.670 14.080 11514 Z= 0.353 Chirality : 0.045 0.181 1290 Planarity : 0.006 0.142 1490 Dihedral : 5.629 35.444 1159 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.97 % Favored : 91.75 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.25), residues: 1059 helix: -2.35 (0.61), residues: 49 sheet: -0.61 (0.28), residues: 312 loop : -1.35 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 353 HIS 0.005 0.001 HIS H 208 PHE 0.027 0.002 PHE H 108 TYR 0.023 0.002 TYR H 33 ARG 0.033 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 104 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8706 (p0) cc_final: 0.8456 (p0) REVERT: A 392 PHE cc_start: 0.7781 (m-80) cc_final: 0.6922 (m-80) REVERT: H 20 LEU cc_start: 0.9524 (mt) cc_final: 0.9289 (mt) REVERT: H 32 TYR cc_start: 0.7305 (m-80) cc_final: 0.6931 (m-80) REVERT: H 158 VAL cc_start: 0.7916 (m) cc_final: 0.7480 (p) REVERT: L 70 ASP cc_start: 0.8947 (p0) cc_final: 0.8728 (p0) REVERT: L 71 PHE cc_start: 0.6966 (m-80) cc_final: 0.5987 (m-10) REVERT: L 175 LEU cc_start: 0.8905 (tp) cc_final: 0.8522 (tp) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1898 time to fit residues: 28.2361 Evaluate side-chains 74 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 0.5980 chunk 1 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 87 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 52 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 34 optimal weight: 0.2980 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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 196 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN ** L 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 8449 Z= 0.302 Angle : 0.740 13.895 11514 Z= 0.391 Chirality : 0.046 0.186 1290 Planarity : 0.006 0.134 1490 Dihedral : 6.215 36.062 1159 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 25.15 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.58 % Favored : 90.13 % 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 : 0.39 % 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: -1.93 (0.24), residues: 1059 helix: -2.76 (0.51), residues: 60 sheet: -0.88 (0.28), residues: 314 loop : -1.36 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP A 353 HIS 0.008 0.002 HIS H 102 PHE 0.024 0.002 PHE H 108 TYR 0.021 0.002 TYR A 449 ARG 0.035 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 fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.8564 (m-80) cc_final: 0.8297 (m-80) REVERT: A 392 PHE cc_start: 0.7781 (m-80) cc_final: 0.6967 (m-80) REVERT: H 36 TRP cc_start: 0.8572 (m100) cc_final: 0.7352 (m100) REVERT: H 153 TYR cc_start: 0.8215 (p90) cc_final: 0.7793 (p90) REVERT: L 71 PHE cc_start: 0.7521 (m-80) cc_final: 0.6542 (m-10) REVERT: L 169 LYS cc_start: 0.9731 (mmmt) cc_final: 0.9047 (tmtt) REVERT: L 175 LEU cc_start: 0.8978 (tp) cc_final: 0.8305 (tp) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1777 time to fit residues: 23.3800 Evaluate side-chains 62 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 85 optimal weight: 0.0030 chunk 47 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 98 optimal weight: 6.9990 overall best weight: 2.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 8449 Z= 0.322 Angle : 0.785 14.242 11514 Z= 0.415 Chirality : 0.046 0.196 1290 Planarity : 0.006 0.103 1490 Dihedral : 6.622 35.084 1159 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 30.38 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.49 % Favored : 90.23 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -2.13 (0.24), residues: 1059 helix: -2.78 (0.54), residues: 57 sheet: -0.79 (0.29), residues: 282 loop : -1.63 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 353 HIS 0.011 0.002 HIS H 102 PHE 0.031 0.003 PHE H 108 TYR 0.041 0.003 TYR H 33 ARG 0.028 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 90 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.8737 (m-80) cc_final: 0.8525 (m-80) REVERT: A 392 PHE cc_start: 0.7740 (m-80) cc_final: 0.6968 (m-80) REVERT: A 396 TYR cc_start: 0.9188 (m-10) cc_final: 0.8779 (m-10) REVERT: H 36 TRP cc_start: 0.8634 (m100) cc_final: 0.7731 (m100) REVERT: H 153 TYR cc_start: 0.8416 (p90) cc_final: 0.7683 (p90) REVERT: H 219 VAL cc_start: 0.8169 (t) cc_final: 0.7791 (t) REVERT: L 169 LYS cc_start: 0.9738 (mmmt) cc_final: 0.9084 (tmtt) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1815 time to fit residues: 24.1641 Evaluate side-chains 64 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 57 optimal weight: 0.0370 chunk 102 optimal weight: 0.8980 chunk 63 optimal weight: 0.0470 chunk 62 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 8449 Z= 0.210 Angle : 0.697 15.094 11514 Z= 0.363 Chirality : 0.046 0.173 1290 Planarity : 0.006 0.100 1490 Dihedral : 6.013 33.957 1159 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.73 % Favored : 90.99 % 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: -1.93 (0.25), residues: 1059 helix: -2.73 (0.56), residues: 57 sheet: -0.76 (0.29), residues: 287 loop : -1.43 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP L 94 HIS 0.003 0.001 HIS H 208 PHE 0.025 0.002 PHE H 108 TYR 0.018 0.002 TYR A 423 ARG 0.027 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 98 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.8625 (m-80) cc_final: 0.8245 (m-80) REVERT: A 364 ASP cc_start: 0.8767 (p0) cc_final: 0.8563 (p0) REVERT: A 392 PHE cc_start: 0.7770 (m-80) cc_final: 0.6896 (m-80) REVERT: A 418 ILE cc_start: 0.9183 (pt) cc_final: 0.8856 (mm) REVERT: H 153 TYR cc_start: 0.8415 (p90) cc_final: 0.7696 (p90) REVERT: H 216 ASP cc_start: 0.7564 (m-30) cc_final: 0.7244 (m-30) REVERT: H 219 VAL cc_start: 0.8022 (t) cc_final: 0.7707 (t) REVERT: L 71 PHE cc_start: 0.7364 (m-80) cc_final: 0.7021 (m-80) REVERT: L 169 LYS cc_start: 0.9724 (mmmt) cc_final: 0.9507 (mmmm) REVERT: L 175 LEU cc_start: 0.9125 (tp) cc_final: 0.8841 (tp) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1882 time to fit residues: 26.7233 Evaluate side-chains 70 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 69 optimal weight: 0.4980 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 196 ASN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8449 Z= 0.187 Angle : 0.678 15.034 11514 Z= 0.351 Chirality : 0.045 0.170 1290 Planarity : 0.006 0.111 1490 Dihedral : 5.708 32.809 1159 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.63 % Favored : 91.08 % 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 : 0.20 % 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: -1.87 (0.25), residues: 1059 helix: -2.25 (0.59), residues: 61 sheet: -0.83 (0.29), residues: 300 loop : -1.37 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 353 HIS 0.004 0.001 HIS A 69 PHE 0.023 0.002 PHE H 108 TYR 0.017 0.002 TYR H 33 ARG 0.025 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 98 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.8555 (m-80) cc_final: 0.8208 (m-80) REVERT: A 392 PHE cc_start: 0.7701 (m-80) cc_final: 0.6778 (m-80) REVERT: A 418 ILE cc_start: 0.9158 (pt) cc_final: 0.8873 (mm) REVERT: H 153 TYR cc_start: 0.8404 (p90) cc_final: 0.7622 (p90) REVERT: H 219 VAL cc_start: 0.8121 (t) cc_final: 0.7844 (t) REVERT: L 4 MET cc_start: 0.9047 (mpp) cc_final: 0.8688 (mpp) REVERT: L 71 PHE cc_start: 0.7194 (m-80) cc_final: 0.6804 (m-80) REVERT: L 165 GLU cc_start: 0.9238 (mm-30) cc_final: 0.8995 (mp0) REVERT: L 175 LEU cc_start: 0.9126 (tp) cc_final: 0.8844 (tp) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1855 time to fit residues: 26.2386 Evaluate side-chains 71 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 62 optimal weight: 0.3980 chunk 100 optimal weight: 6.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.5565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 8449 Z= 0.338 Angle : 0.815 19.227 11514 Z= 0.427 Chirality : 0.047 0.186 1290 Planarity : 0.006 0.128 1490 Dihedral : 6.540 35.450 1159 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 29.88 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.86 % Favored : 87.95 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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: -2.19 (0.25), residues: 1059 helix: -2.52 (0.58), residues: 61 sheet: -1.11 (0.27), residues: 338 loop : -1.56 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP H 36 HIS 0.007 0.002 HIS H 172 PHE 0.043 0.003 PHE L 71 TYR 0.032 0.003 TYR H 33 ARG 0.033 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 82 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6542 (mtp) cc_final: 0.6298 (mtp) REVERT: A 392 PHE cc_start: 0.7722 (m-80) cc_final: 0.6796 (m-80) REVERT: A 418 ILE cc_start: 0.9187 (pt) cc_final: 0.8921 (mm) REVERT: H 32 TYR cc_start: 0.6399 (m-10) cc_final: 0.6087 (m-80) REVERT: H 153 TYR cc_start: 0.8667 (p90) cc_final: 0.7795 (p90) REVERT: H 219 VAL cc_start: 0.8184 (t) cc_final: 0.7766 (t) REVERT: L 165 GLU cc_start: 0.9273 (mm-30) cc_final: 0.8766 (mm-30) REVERT: L 175 LEU cc_start: 0.9194 (tp) cc_final: 0.8882 (tp) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1917 time to fit residues: 22.7727 Evaluate side-chains 58 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 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 61 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 105 optimal weight: 6.9990 chunk 97 optimal weight: 0.0370 chunk 84 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 64 optimal weight: 0.0970 chunk 51 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.4656 ------------------------------------------------------------------------------- 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 563 GLN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.5608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 8449 Z= 0.191 Angle : 0.715 15.885 11514 Z= 0.367 Chirality : 0.047 0.187 1290 Planarity : 0.005 0.096 1490 Dihedral : 5.867 33.213 1159 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.63 % Favored : 91.18 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % 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: -1.87 (0.25), residues: 1059 helix: -2.40 (0.58), residues: 61 sheet: -0.91 (0.29), residues: 324 loop : -1.32 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP L 94 HIS 0.004 0.001 HIS A 69 PHE 0.030 0.002 PHE H 108 TYR 0.027 0.002 TYR H 33 ARG 0.038 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 88 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.7697 (m-80) cc_final: 0.6914 (m-80) REVERT: A 418 ILE cc_start: 0.9129 (pt) cc_final: 0.8879 (mm) REVERT: H 153 TYR cc_start: 0.8501 (p90) cc_final: 0.7763 (p90) REVERT: L 175 LEU cc_start: 0.9115 (tp) cc_final: 0.8756 (tp) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1868 time to fit residues: 24.0052 Evaluate side-chains 58 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 0.2980 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 84 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.070209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.052653 restraints weight = 139606.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.055318 restraints weight = 77540.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.057174 restraints weight = 50598.011| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.5798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 8449 Z= 0.237 Angle : 0.720 15.418 11514 Z= 0.374 Chirality : 0.046 0.184 1290 Planarity : 0.006 0.111 1490 Dihedral : 5.937 35.157 1159 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 22.56 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.44 % Favored : 89.37 % 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: -2.29 (0.60), residues: 61 sheet: -1.02 (0.28), residues: 333 loop : -1.40 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP L 94 HIS 0.005 0.001 HIS H 172 PHE 0.029 0.002 PHE H 108 TYR 0.025 0.002 TYR H 33 ARG 0.036 0.001 ARG H 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2177.02 seconds wall clock time: 40 minutes 29.30 seconds (2429.30 seconds total)