Starting phenix.real_space_refine on Sat Aug 3 17:09:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tpn_41478/08_2024/8tpn_41478.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tpn_41478/08_2024/8tpn_41478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tpn_41478/08_2024/8tpn_41478.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tpn_41478/08_2024/8tpn_41478.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tpn_41478/08_2024/8tpn_41478.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tpn_41478/08_2024/8tpn_41478.cif" } resolution = 4.07 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= 0.001 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: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 36 5.16 5 C 5662 2.51 5 N 1414 2.21 5 O 1496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 114": "OE1" <-> "OE2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A GLU 491": "OE1" <-> "OE2" Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 114": "OE1" <-> "OE2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "B GLU 262": "OE1" <-> "OE2" Residue "B GLU 491": "OE1" <-> "OE2" Residue "B TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8612 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4304 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 21, 'TRANS': 529} Chain breaks: 8 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 9, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 114 Chain: "B" Number of atoms: 4304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4304 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 21, 'TRANS': 529} Chain breaks: 8 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 9, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 114 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.09, per 1000 atoms: 0.59 Number of scatterers: 8612 At special positions: 0 Unit cell: (111.93, 115.57, 96.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 36 16.00 O 1496 8.00 N 1414 7.00 C 5662 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.34 Conformation dependent library (CDL) restraints added in 1.4 seconds 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 2 sheets defined 74.4% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 32 through 50 removed outlier: 3.511A pdb=" N VAL A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 90 Processing helix chain 'A' and resid 103 through 108 removed outlier: 4.438A pdb=" N ASP A 107 " --> pdb=" O GLN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 125 Processing helix chain 'A' and resid 126 through 130 Processing helix chain 'A' and resid 152 through 164 Processing helix chain 'A' and resid 170 through 182 removed outlier: 3.775A pdb=" N ILE A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 199 Processing helix chain 'A' and resid 199 through 212 Processing helix chain 'A' and resid 217 through 246 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 280 through 289 removed outlier: 3.948A pdb=" N ARG A 284 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 317 removed outlier: 3.640A pdb=" N PHE A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 358 Proline residue: A 341 - end of helix removed outlier: 3.542A pdb=" N VAL A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 392 removed outlier: 5.643A pdb=" N ALA A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 392 " --> pdb=" O PHE A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 411 removed outlier: 3.721A pdb=" N ALA A 411 " --> pdb=" O TRP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 449 removed outlier: 3.607A pdb=" N TYR A 439 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ALA A 444 " --> pdb=" O PHE A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 465 Processing helix chain 'A' and resid 482 through 494 removed outlier: 3.873A pdb=" N THR A 494 " --> pdb=" O ARG A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 518 removed outlier: 3.614A pdb=" N SER A 518 " --> pdb=" O VAL A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 545 removed outlier: 3.856A pdb=" N CYS A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 530 " --> pdb=" O CYS A 526 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ARG A 537 " --> pdb=" O TRP A 533 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 584 removed outlier: 3.670A pdb=" N ALA A 564 " --> pdb=" O PRO A 560 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 578 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 584 " --> pdb=" O VAL A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 625 removed outlier: 3.590A pdb=" N SER A 625 " --> pdb=" O ARG A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 711 Processing helix chain 'B' and resid 32 through 50 removed outlier: 3.511A pdb=" N VAL B 50 " --> pdb=" O ALA B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 90 Processing helix chain 'B' and resid 103 through 108 removed outlier: 4.437A pdb=" N ASP B 107 " --> pdb=" O GLN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 125 Processing helix chain 'B' and resid 126 through 130 Processing helix chain 'B' and resid 152 through 164 Processing helix chain 'B' and resid 170 through 182 removed outlier: 3.775A pdb=" N ILE B 174 " --> pdb=" O GLU B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 199 Processing helix chain 'B' and resid 199 through 212 Processing helix chain 'B' and resid 217 through 246 Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.948A pdb=" N ARG B 284 " --> pdb=" O PRO B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 317 removed outlier: 3.640A pdb=" N PHE B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 358 Proline residue: B 341 - end of helix removed outlier: 3.542A pdb=" N VAL B 346 " --> pdb=" O THR B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 392 removed outlier: 5.644A pdb=" N ALA B 385 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LEU B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 411 removed outlier: 3.721A pdb=" N ALA B 411 " --> pdb=" O TRP B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 449 removed outlier: 3.607A pdb=" N TYR B 439 " --> pdb=" O ASN B 435 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ALA B 444 " --> pdb=" O PHE B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 465 Processing helix chain 'B' and resid 482 through 494 removed outlier: 3.872A pdb=" N THR B 494 " --> pdb=" O ARG B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 518 removed outlier: 3.614A pdb=" N SER B 518 " --> pdb=" O VAL B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 545 removed outlier: 3.855A pdb=" N CYS B 527 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 530 " --> pdb=" O CYS B 526 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ARG B 537 " --> pdb=" O TRP B 533 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ALA B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 584 removed outlier: 3.670A pdb=" N ALA B 564 " --> pdb=" O PRO B 560 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER B 577 " --> pdb=" O SER B 573 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA B 578 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 625 removed outlier: 3.590A pdb=" N SER B 625 " --> pdb=" O ARG B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 711 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56 Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 56 598 hydrogen bonds defined for protein. 1758 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: 2.33 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2670 1.34 - 1.46: 2218 1.46 - 1.58: 3886 1.58 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 8832 Sorted by residual: bond pdb=" C VAL B 455 " pdb=" N PRO B 456 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.36e-02 5.41e+03 6.47e-01 bond pdb=" C ILE B 394 " pdb=" N PRO B 395 " ideal model delta sigma weight residual 1.335 1.345 -0.010 1.28e-02 6.10e+03 6.40e-01 bond pdb=" C VAL A 455 " pdb=" N PRO A 456 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.36e-02 5.41e+03 6.38e-01 bond pdb=" C PHE A 181 " pdb=" N GLY A 182 " ideal model delta sigma weight residual 1.335 1.329 0.006 7.50e-03 1.78e+04 6.36e-01 bond pdb=" C ILE A 394 " pdb=" N PRO A 395 " ideal model delta sigma weight residual 1.335 1.345 -0.010 1.28e-02 6.10e+03 6.05e-01 ... (remaining 8827 not shown) Histogram of bond angle deviations from ideal: 100.17 - 106.94: 240 106.94 - 113.70: 4866 113.70 - 120.47: 3556 120.47 - 127.23: 3253 127.23 - 134.00: 113 Bond angle restraints: 12028 Sorted by residual: angle pdb=" N GLY A 182 " pdb=" CA GLY A 182 " pdb=" C GLY A 182 " ideal model delta sigma weight residual 111.21 114.35 -3.14 1.04e+00 9.25e-01 9.09e+00 angle pdb=" N GLY B 182 " pdb=" CA GLY B 182 " pdb=" C GLY B 182 " ideal model delta sigma weight residual 111.21 114.31 -3.10 1.04e+00 9.25e-01 8.89e+00 angle pdb=" CA VAL A 455 " pdb=" C VAL A 455 " pdb=" N PRO A 456 " ideal model delta sigma weight residual 118.88 122.02 -3.14 1.54e+00 4.22e-01 4.15e+00 angle pdb=" CA VAL B 455 " pdb=" C VAL B 455 " pdb=" N PRO B 456 " ideal model delta sigma weight residual 118.88 121.99 -3.11 1.54e+00 4.22e-01 4.07e+00 angle pdb=" C PHE B 181 " pdb=" N GLY B 182 " pdb=" CA GLY B 182 " ideal model delta sigma weight residual 122.63 120.64 1.99 1.03e+00 9.43e-01 3.73e+00 ... (remaining 12023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 4514 17.92 - 35.85: 480 35.85 - 53.77: 82 53.77 - 71.69: 12 71.69 - 89.62: 10 Dihedral angle restraints: 5098 sinusoidal: 1880 harmonic: 3218 Sorted by residual: dihedral pdb=" CA THR A 441 " pdb=" C THR A 441 " pdb=" N VAL A 442 " pdb=" CA VAL A 442 " ideal model delta harmonic sigma weight residual -180.00 -163.13 -16.87 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA THR B 441 " pdb=" C THR B 441 " pdb=" N VAL B 442 " pdb=" CA VAL B 442 " ideal model delta harmonic sigma weight residual -180.00 -163.13 -16.87 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CB GLU A 452 " pdb=" CG GLU A 452 " pdb=" CD GLU A 452 " pdb=" OE1 GLU A 452 " ideal model delta sinusoidal sigma weight residual 0.00 89.62 -89.62 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 5095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 928 0.030 - 0.060: 289 0.060 - 0.091: 116 0.091 - 0.121: 35 0.121 - 0.151: 6 Chirality restraints: 1374 Sorted by residual: chirality pdb=" CA THR A 340 " pdb=" N THR A 340 " pdb=" C THR A 340 " pdb=" CB THR A 340 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA THR B 340 " pdb=" N THR B 340 " pdb=" C THR B 340 " pdb=" CB THR B 340 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.64e-01 chirality pdb=" CA ILE A 147 " pdb=" N ILE A 147 " pdb=" C ILE A 147 " pdb=" CB ILE A 147 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 1371 not shown) Planarity restraints: 1496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 292 " -0.051 5.00e-02 4.00e+02 7.61e-02 9.27e+00 pdb=" N PRO A 293 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 293 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 293 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 292 " -0.051 5.00e-02 4.00e+02 7.61e-02 9.26e+00 pdb=" N PRO B 293 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 293 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 293 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 439 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.91e+00 pdb=" C TYR A 439 " 0.029 2.00e-02 2.50e+03 pdb=" O TYR A 439 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE A 440 " -0.010 2.00e-02 2.50e+03 ... (remaining 1493 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1291 2.76 - 3.29: 8532 3.29 - 3.83: 14341 3.83 - 4.36: 13948 4.36 - 4.90: 25865 Nonbonded interactions: 63977 Sorted by model distance: nonbonded pdb=" OG1 THR B 362 " pdb=" OD1 ASP B 364 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR A 362 " pdb=" OD1 ASP A 364 " model vdw 2.220 3.040 nonbonded pdb=" OH TYR A 26 " pdb=" O ALA A 36 " model vdw 2.229 3.040 nonbonded pdb=" OH TYR B 26 " pdb=" O ALA B 36 " model vdw 2.229 3.040 nonbonded pdb=" OH TYR A 188 " pdb=" OD2 ASP A 539 " model vdw 2.235 3.040 ... (remaining 63972 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.510 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 : 0.002 0.034 8832 Z= 0.150 Angle : 0.464 6.861 12028 Z= 0.249 Chirality : 0.037 0.151 1374 Planarity : 0.004 0.076 1496 Dihedral : 15.102 89.616 3002 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.26), residues: 1066 helix: 2.61 (0.19), residues: 750 sheet: 0.63 (0.91), residues: 48 loop : -0.56 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.002 0.000 HIS B 611 PHE 0.011 0.001 PHE A 187 TYR 0.009 0.001 TYR B 218 ARG 0.001 0.000 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.903 Fit side-chains REVERT: A 456 PRO cc_start: 0.8284 (Cg_exo) cc_final: 0.8061 (Cg_endo) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1749 time to fit residues: 29.4917 Evaluate side-chains 87 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 128 ASN A 374 GLN B 79 GLN B 128 ASN B 374 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8832 Z= 0.214 Angle : 0.495 7.155 12028 Z= 0.267 Chirality : 0.039 0.148 1374 Planarity : 0.004 0.060 1496 Dihedral : 3.549 15.120 1166 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.26), residues: 1066 helix: 2.55 (0.18), residues: 766 sheet: 0.62 (0.91), residues: 48 loop : -0.59 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 521 HIS 0.003 0.001 HIS A 127 PHE 0.010 0.001 PHE A 198 TYR 0.008 0.001 TYR B 220 ARG 0.003 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.958 Fit side-chains REVERT: A 286 LYS cc_start: 0.8301 (ttmt) cc_final: 0.7908 (tppt) REVERT: A 456 PRO cc_start: 0.8367 (Cg_exo) cc_final: 0.8114 (Cg_endo) REVERT: B 122 MET cc_start: 0.8547 (ttm) cc_final: 0.8301 (ttm) REVERT: B 286 LYS cc_start: 0.8442 (ttmt) cc_final: 0.8129 (tppt) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1751 time to fit residues: 30.1837 Evaluate side-chains 89 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 5.9990 chunk 31 optimal weight: 0.0010 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8832 Z= 0.192 Angle : 0.482 7.176 12028 Z= 0.258 Chirality : 0.039 0.166 1374 Planarity : 0.004 0.053 1496 Dihedral : 3.573 16.626 1166 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.26), residues: 1066 helix: 2.48 (0.18), residues: 766 sheet: 0.65 (0.92), residues: 48 loop : -0.62 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 521 HIS 0.002 0.001 HIS B 58 PHE 0.011 0.001 PHE A 40 TYR 0.009 0.001 TYR B 234 ARG 0.006 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 LYS cc_start: 0.8294 (ttmt) cc_final: 0.7898 (tppt) REVERT: B 286 LYS cc_start: 0.8393 (ttmt) cc_final: 0.8070 (tppt) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1756 time to fit residues: 30.6213 Evaluate side-chains 88 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 51 optimal weight: 0.0670 chunk 11 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8832 Z= 0.190 Angle : 0.489 7.370 12028 Z= 0.259 Chirality : 0.038 0.153 1374 Planarity : 0.004 0.048 1496 Dihedral : 3.582 15.712 1166 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.26), residues: 1066 helix: 2.39 (0.18), residues: 766 sheet: 0.57 (0.91), residues: 48 loop : -0.71 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 521 HIS 0.001 0.001 HIS A 58 PHE 0.011 0.001 PHE A 40 TYR 0.009 0.001 TYR A 234 ARG 0.007 0.000 ARG B 432 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 286 LYS cc_start: 0.8293 (ttmt) cc_final: 0.7898 (tppt) REVERT: B 286 LYS cc_start: 0.8343 (ttmt) cc_final: 0.8012 (tppt) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1767 time to fit residues: 29.7819 Evaluate side-chains 86 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 79 optimal weight: 0.0980 chunk 43 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 95 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8832 Z= 0.164 Angle : 0.470 7.136 12028 Z= 0.248 Chirality : 0.038 0.148 1374 Planarity : 0.004 0.044 1496 Dihedral : 3.549 15.524 1166 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.26), residues: 1066 helix: 2.42 (0.18), residues: 766 sheet: 0.58 (0.92), residues: 48 loop : -0.72 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 521 HIS 0.001 0.001 HIS A 366 PHE 0.011 0.001 PHE A 40 TYR 0.010 0.001 TYR B 234 ARG 0.004 0.000 ARG B 432 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.961 Fit side-chains REVERT: A 286 LYS cc_start: 0.8278 (ttmt) cc_final: 0.7890 (tppt) REVERT: B 286 LYS cc_start: 0.8307 (ttmt) cc_final: 0.7996 (tppt) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1731 time to fit residues: 29.1242 Evaluate side-chains 87 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 102 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 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8832 Z= 0.347 Angle : 0.607 7.443 12028 Z= 0.331 Chirality : 0.042 0.152 1374 Planarity : 0.005 0.041 1496 Dihedral : 4.014 15.827 1166 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.25), residues: 1066 helix: 1.95 (0.18), residues: 762 sheet: 0.24 (0.90), residues: 48 loop : -1.01 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 521 HIS 0.004 0.001 HIS B 401 PHE 0.016 0.002 PHE A 189 TYR 0.015 0.002 TYR B 220 ARG 0.004 0.000 ARG B 432 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.106 Fit side-chains revert: symmetry clash REVERT: A 286 LYS cc_start: 0.8345 (ttmt) cc_final: 0.7912 (tppt) REVERT: A 531 ASN cc_start: 0.8007 (t0) cc_final: 0.7767 (t0) REVERT: B 286 LYS cc_start: 0.8393 (ttmt) cc_final: 0.7955 (tppt) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1707 time to fit residues: 27.4035 Evaluate side-chains 81 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 59 optimal weight: 0.0020 chunk 106 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 64 optimal weight: 0.1980 chunk 48 optimal weight: 0.9990 chunk 65 optimal weight: 0.0050 chunk 42 optimal weight: 0.1980 overall best weight: 0.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 ASN B 374 GLN B 531 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8832 Z= 0.142 Angle : 0.492 6.898 12028 Z= 0.258 Chirality : 0.038 0.153 1374 Planarity : 0.004 0.040 1496 Dihedral : 3.684 15.694 1166 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.26), residues: 1066 helix: 2.29 (0.18), residues: 764 sheet: 0.44 (0.91), residues: 48 loop : -0.92 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 88 HIS 0.001 0.000 HIS A 366 PHE 0.011 0.001 PHE B 511 TYR 0.017 0.002 TYR A 513 ARG 0.006 0.000 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.955 Fit side-chains REVERT: A 286 LYS cc_start: 0.8254 (ttmt) cc_final: 0.7887 (tppt) REVERT: A 456 PRO cc_start: 0.8224 (Cg_exo) cc_final: 0.8021 (Cg_endo) REVERT: B 41 VAL cc_start: 0.9084 (t) cc_final: 0.8803 (p) REVERT: B 286 LYS cc_start: 0.8282 (ttmt) cc_final: 0.7934 (tppt) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1779 time to fit residues: 30.4850 Evaluate side-chains 86 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 83 optimal weight: 0.0870 chunk 96 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN B 531 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8832 Z= 0.172 Angle : 0.483 7.393 12028 Z= 0.255 Chirality : 0.038 0.150 1374 Planarity : 0.004 0.039 1496 Dihedral : 3.598 14.850 1166 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.26), residues: 1066 helix: 2.30 (0.18), residues: 764 sheet: 0.51 (0.92), residues: 48 loop : -0.95 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 521 HIS 0.005 0.001 HIS A 151 PHE 0.010 0.001 PHE A 40 TYR 0.012 0.001 TYR A 234 ARG 0.004 0.000 ARG B 432 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.917 Fit side-chains REVERT: A 286 LYS cc_start: 0.8256 (ttmt) cc_final: 0.7887 (tppt) REVERT: B 286 LYS cc_start: 0.8317 (ttmt) cc_final: 0.7952 (tppt) REVERT: B 521 TRP cc_start: 0.8738 (t60) cc_final: 0.8525 (t60) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1726 time to fit residues: 27.6177 Evaluate side-chains 81 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8832 Z= 0.229 Angle : 0.514 7.427 12028 Z= 0.274 Chirality : 0.040 0.168 1374 Planarity : 0.004 0.038 1496 Dihedral : 3.726 15.352 1166 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.26), residues: 1066 helix: 2.22 (0.18), residues: 764 sheet: 0.38 (0.91), residues: 48 loop : -1.06 (0.35), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 521 HIS 0.003 0.001 HIS A 151 PHE 0.017 0.001 PHE A 198 TYR 0.008 0.001 TYR A 383 ARG 0.004 0.000 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.958 Fit side-chains REVERT: A 286 LYS cc_start: 0.8352 (ttmt) cc_final: 0.7888 (tppt) REVERT: B 286 LYS cc_start: 0.8320 (ttmt) cc_final: 0.7934 (tppt) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1706 time to fit residues: 27.3844 Evaluate side-chains 83 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 109 optimal weight: 20.0000 chunk 100 optimal weight: 0.5980 chunk 87 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 0.0270 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8832 Z= 0.179 Angle : 0.506 7.359 12028 Z= 0.263 Chirality : 0.039 0.165 1374 Planarity : 0.004 0.038 1496 Dihedral : 3.684 15.285 1166 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.11 % Allowed : 0.11 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.26), residues: 1066 helix: 2.31 (0.18), residues: 764 sheet: 0.28 (0.89), residues: 48 loop : -1.08 (0.35), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 521 HIS 0.002 0.001 HIS A 151 PHE 0.013 0.001 PHE A 388 TYR 0.008 0.001 TYR B 383 ARG 0.003 0.000 ARG B 432 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 0.969 Fit side-chains REVERT: A 286 LYS cc_start: 0.8272 (ttmt) cc_final: 0.7880 (tppt) REVERT: B 286 LYS cc_start: 0.8312 (ttmt) cc_final: 0.7942 (tppt) outliers start: 1 outliers final: 0 residues processed: 108 average time/residue: 0.1756 time to fit residues: 27.7631 Evaluate side-chains 83 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 ASN ** 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 = 0.3443 r_free = 0.3443 target = 0.123140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.103419 restraints weight = 14719.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.104306 restraints weight = 12018.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.104741 restraints weight = 10428.283| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8832 Z= 0.262 Angle : 0.540 7.584 12028 Z= 0.288 Chirality : 0.041 0.168 1374 Planarity : 0.004 0.038 1496 Dihedral : 3.834 15.384 1166 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.26), residues: 1066 helix: 2.17 (0.18), residues: 764 sheet: 0.22 (0.89), residues: 48 loop : -1.16 (0.35), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 521 HIS 0.007 0.001 HIS B 151 PHE 0.015 0.001 PHE A 187 TYR 0.009 0.002 TYR B 383 ARG 0.004 0.000 ARG B 549 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1677.06 seconds wall clock time: 30 minutes 38.02 seconds (1838.02 seconds total)