Starting phenix.real_space_refine on Mon Mar 11 16:18:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wba_37418/03_2024/8wba_37418.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wba_37418/03_2024/8wba_37418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wba_37418/03_2024/8wba_37418.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wba_37418/03_2024/8wba_37418.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wba_37418/03_2024/8wba_37418.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wba_37418/03_2024/8wba_37418.pdb" } resolution = 3.1 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= -0.002 sd= 0.080 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 58 5.16 5 C 5646 2.51 5 N 1430 2.21 5 O 1512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 44": "OD1" <-> "OD2" Residue "A ASP 148": "OD1" <-> "OD2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 44": "OD1" <-> "OD2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B GLU 232": "OE1" <-> "OE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 300": "OE1" <-> "OE2" Residue "B PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 8646 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4288 Classifications: {'peptide': 553} Link IDs: {'PTRANS': 18, 'TRANS': 534} Chain breaks: 4 Chain: "B" Number of atoms: 4288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4288 Classifications: {'peptide': 553} Link IDs: {'PTRANS': 18, 'TRANS': 534} Chain breaks: 4 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.15, per 1000 atoms: 0.60 Number of scatterers: 8646 At special positions: 0 Unit cell: (68.2, 105.6, 122.1, 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 58 16.00 O 1512 8.00 N 1430 7.00 C 5646 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 606 " - pdb=" SG CYS A 622 " distance=2.03 Simple disulfide: pdb=" SG CYS B 606 " - pdb=" SG CYS B 622 " 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: 3.63 Conformation dependent library (CDL) restraints added in 1.8 seconds 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2028 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 5 sheets defined 66.1% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 106 through 115 Processing helix chain 'A' and resid 135 through 140 removed outlier: 3.538A pdb=" N LYS A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 169 Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'A' and resid 190 through 194 removed outlier: 4.184A pdb=" N LYS A 193 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 220 Processing helix chain 'A' and resid 238 through 255 Processing helix chain 'A' and resid 268 through 275 removed outlier: 3.596A pdb=" N PHE A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 311 through 321 Processing helix chain 'A' and resid 338 through 357 removed outlier: 4.832A pdb=" N ALA A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) Proline residue: A 351 - end of helix Processing helix chain 'A' and resid 379 through 406 removed outlier: 4.569A pdb=" N LYS A 399 " --> pdb=" O HIS A 395 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLU A 400 " --> pdb=" O ARG A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 Processing helix chain 'A' and resid 432 through 456 Proline residue: A 451 - end of helix removed outlier: 3.683A pdb=" N VAL A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 469 removed outlier: 3.620A pdb=" N GLU A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA A 464 " --> pdb=" O PRO A 460 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ILE A 465 " --> pdb=" O GLN A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 492 Processing helix chain 'A' and resid 493 through 508 removed outlier: 4.020A pdb=" N TRP A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 541 removed outlier: 3.746A pdb=" N ILE A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 561 Processing helix chain 'A' and resid 575 through 579 Processing helix chain 'A' and resid 580 through 595 Processing helix chain 'A' and resid 597 through 605 Processing helix chain 'A' and resid 619 through 630 removed outlier: 3.635A pdb=" N VAL A 625 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU A 628 " --> pdb=" O PHE A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 660 removed outlier: 3.753A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'B' and resid 156 through 169 Processing helix chain 'B' and resid 174 through 189 Processing helix chain 'B' and resid 190 through 194 removed outlier: 4.082A pdb=" N LYS B 193 " --> pdb=" O GLY B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 220 removed outlier: 3.514A pdb=" N GLU B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 255 Processing helix chain 'B' and resid 268 through 275 removed outlier: 3.650A pdb=" N PHE B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 311 through 321 Processing helix chain 'B' and resid 338 through 357 removed outlier: 4.612A pdb=" N ALA B 350 " --> pdb=" O ASP B 346 " (cutoff:3.500A) Proline residue: B 351 - end of helix Processing helix chain 'B' and resid 379 through 405 removed outlier: 4.583A pdb=" N LYS B 399 " --> pdb=" O HIS B 395 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLU B 400 " --> pdb=" O ARG B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 425 Processing helix chain 'B' and resid 432 through 456 Proline residue: B 451 - end of helix Processing helix chain 'B' and resid 457 through 472 removed outlier: 4.979A pdb=" N ALA B 464 " --> pdb=" O PRO B 460 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ILE B 465 " --> pdb=" O GLN B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 492 Processing helix chain 'B' and resid 493 through 508 removed outlier: 4.170A pdb=" N TRP B 505 " --> pdb=" O THR B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 541 removed outlier: 3.628A pdb=" N ILE B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 561 Processing helix chain 'B' and resid 573 through 578 removed outlier: 4.232A pdb=" N LYS B 577 " --> pdb=" O MET B 573 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR B 578 " --> pdb=" O VAL B 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 573 through 578' Processing helix chain 'B' and resid 580 through 595 Processing helix chain 'B' and resid 597 through 605 Processing helix chain 'B' and resid 619 through 625 removed outlier: 3.539A pdb=" N VAL B 625 " --> pdb=" O GLY B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 660 removed outlier: 3.629A pdb=" N VAL B 639 " --> pdb=" O MET B 635 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG B 650 " --> pdb=" O PHE B 646 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 91 removed outlier: 5.209A pdb=" N PHE A 42 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LEU A 128 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ASP A 44 " --> pdb=" O LYS A 126 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS A 126 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 227 through 230 removed outlier: 6.171A pdb=" N LEU A 228 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N PHE A 96 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU A 279 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA A 98 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU A 281 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU A 100 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE A 288 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N SER A 282 " --> pdb=" O CYS A 286 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N CYS A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 87 through 91 removed outlier: 5.401A pdb=" N VAL B 87 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 99 through 100 removed outlier: 5.938A pdb=" N SER B 282 " --> pdb=" O CYS B 286 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N CYS B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 142 through 145 removed outlier: 6.632A pdb=" N GLY B 143 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU B 228 " --> pdb=" O VAL B 261 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 529 hydrogen bonds defined for protein. 1560 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: 2.72 Time building geometry restraints manager: 3.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1502 1.33 - 1.45: 2237 1.45 - 1.57: 4996 1.57 - 1.69: 1 1.69 - 1.81: 92 Bond restraints: 8828 Sorted by residual: bond pdb=" CBE Y01 A 702 " pdb=" CBI Y01 A 702 " ideal model delta sigma weight residual 1.550 1.570 -0.020 2.00e-02 2.50e+03 1.01e+00 bond pdb=" CB MET B 603 " pdb=" CG MET B 603 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.87e-01 bond pdb=" CB PHE A 516 " pdb=" CG PHE A 516 " ideal model delta sigma weight residual 1.502 1.522 -0.020 2.30e-02 1.89e+03 7.79e-01 bond pdb=" CB MET A 603 " pdb=" CG MET A 603 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.99e-01 bond pdb=" CB PHE B 516 " pdb=" CG PHE B 516 " ideal model delta sigma weight residual 1.502 1.520 -0.018 2.30e-02 1.89e+03 6.18e-01 ... (remaining 8823 not shown) Histogram of bond angle deviations from ideal: 98.60 - 105.69: 149 105.69 - 112.79: 4883 112.79 - 119.89: 2831 119.89 - 126.98: 4033 126.98 - 134.08: 82 Bond angle restraints: 11978 Sorted by residual: angle pdb=" CB MET B 603 " pdb=" CG MET B 603 " pdb=" SD MET B 603 " ideal model delta sigma weight residual 112.70 121.32 -8.62 3.00e+00 1.11e-01 8.26e+00 angle pdb=" CA PHE B 308 " pdb=" C PHE B 308 " pdb=" N PRO B 309 " ideal model delta sigma weight residual 117.82 120.00 -2.18 7.80e-01 1.64e+00 7.83e+00 angle pdb=" CB MET A 603 " pdb=" CG MET A 603 " pdb=" SD MET A 603 " ideal model delta sigma weight residual 112.70 120.70 -8.00 3.00e+00 1.11e-01 7.10e+00 angle pdb=" CA LEU A 161 " pdb=" CB LEU A 161 " pdb=" CG LEU A 161 " ideal model delta sigma weight residual 116.30 107.31 8.99 3.50e+00 8.16e-02 6.59e+00 angle pdb=" CA ILE A 541 " pdb=" CB ILE A 541 " pdb=" CG1 ILE A 541 " ideal model delta sigma weight residual 110.40 114.68 -4.28 1.70e+00 3.46e-01 6.33e+00 ... (remaining 11973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 4425 16.36 - 32.71: 648 32.71 - 49.07: 172 49.07 - 65.42: 30 65.42 - 81.78: 15 Dihedral angle restraints: 5290 sinusoidal: 2130 harmonic: 3160 Sorted by residual: dihedral pdb=" CB CYS A 606 " pdb=" SG CYS A 606 " pdb=" SG CYS A 622 " pdb=" CB CYS A 622 " ideal model delta sinusoidal sigma weight residual 93.00 142.65 -49.65 1 1.00e+01 1.00e-02 3.38e+01 dihedral pdb=" CA ASP A 148 " pdb=" CB ASP A 148 " pdb=" CG ASP A 148 " pdb=" OD1 ASP A 148 " ideal model delta sinusoidal sigma weight residual -30.00 -89.28 59.28 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP A 607 " pdb=" CB ASP A 607 " pdb=" CG ASP A 607 " pdb=" OD1 ASP A 607 " ideal model delta sinusoidal sigma weight residual -30.00 -89.14 59.14 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 5287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1223 0.055 - 0.110: 190 0.110 - 0.165: 18 0.165 - 0.220: 1 0.220 - 0.275: 2 Chirality restraints: 1434 Sorted by residual: chirality pdb=" CG LEU A 517 " pdb=" CB LEU A 517 " pdb=" CD1 LEU A 517 " pdb=" CD2 LEU A 517 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CBB Y01 A 702 " pdb=" CAC Y01 A 702 " pdb=" CAO Y01 A 702 " pdb=" CBE Y01 A 702 " both_signs ideal model delta sigma weight residual False 2.58 2.34 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CBE Y01 A 702 " pdb=" CAP Y01 A 702 " pdb=" CBB Y01 A 702 " pdb=" CBI Y01 A 702 " both_signs ideal model delta sigma weight residual False 2.57 2.40 0.17 2.00e-01 2.50e+01 7.42e-01 ... (remaining 1431 not shown) Planarity restraints: 1458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 514 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO A 515 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 515 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 515 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 275 " 0.017 2.00e-02 2.50e+03 1.53e-02 4.11e+00 pdb=" CG PHE B 275 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE B 275 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 275 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE B 275 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 275 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 275 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 514 " 0.034 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO B 515 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 515 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 515 " 0.029 5.00e-02 4.00e+02 ... (remaining 1455 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2394 2.81 - 3.33: 8736 3.33 - 3.86: 15301 3.86 - 4.38: 17514 4.38 - 4.90: 30572 Nonbonded interactions: 74517 Sorted by model distance: nonbonded pdb=" NH1 ARG B 168 " pdb=" O HIS B 219 " model vdw 2.289 2.520 nonbonded pdb=" O ALA A 464 " pdb=" OG1 THR A 467 " model vdw 2.352 2.440 nonbonded pdb=" OG SER A 452 " pdb=" O SER A 530 " model vdw 2.357 2.440 nonbonded pdb=" N ILE B 129 " pdb=" O GLY B 132 " model vdw 2.393 2.520 nonbonded pdb=" OE1 GLU A 232 " pdb=" OG SER A 235 " model vdw 2.395 2.440 ... (remaining 74512 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 35 through 660) 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 individual isotropic 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: 1.760 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: 4.190 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 27.280 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 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 0.028 8828 Z= 0.147 Angle : 0.537 8.987 11978 Z= 0.267 Chirality : 0.040 0.275 1434 Planarity : 0.004 0.054 1458 Dihedral : 16.646 81.777 3256 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.32 % Allowed : 25.85 % Favored : 73.82 % 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: 1.56 (0.27), residues: 1086 helix: 1.82 (0.20), residues: 676 sheet: -2.57 (0.55), residues: 68 loop : 0.39 (0.38), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 575 HIS 0.004 0.001 HIS B 154 PHE 0.035 0.002 PHE B 275 TYR 0.009 0.001 TYR B 584 ARG 0.002 0.000 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 131 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 131 average time/residue: 0.2038 time to fit residues: 37.4890 Evaluate side-chains 128 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 601 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN B 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8828 Z= 0.316 Angle : 0.577 8.969 11978 Z= 0.281 Chirality : 0.041 0.227 1434 Planarity : 0.005 0.044 1458 Dihedral : 6.046 59.957 1340 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.70 % Allowed : 21.79 % Favored : 73.50 % 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: 1.30 (0.26), residues: 1086 helix: 1.52 (0.19), residues: 696 sheet: -2.09 (0.62), residues: 58 loop : 0.20 (0.39), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 447 HIS 0.006 0.001 HIS A 219 PHE 0.029 0.002 PHE A 275 TYR 0.012 0.002 TYR A 526 ARG 0.002 0.000 ARG A 410 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 137 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7842 (mmmt) cc_final: 0.7420 (mmmt) REVERT: A 256 LYS cc_start: 0.8335 (mmtt) cc_final: 0.8022 (mmmm) REVERT: B 274 MET cc_start: 0.7961 (mmm) cc_final: 0.7215 (mmt) REVERT: B 291 LYS cc_start: 0.8408 (ttmm) cc_final: 0.7939 (ttpt) REVERT: B 413 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7876 (tt0) REVERT: B 630 ILE cc_start: 0.8034 (mp) cc_final: 0.7696 (mp) REVERT: B 636 TRP cc_start: 0.8129 (m100) cc_final: 0.7724 (m100) outliers start: 44 outliers final: 25 residues processed: 165 average time/residue: 0.1873 time to fit residues: 43.8887 Evaluate side-chains 160 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain B residue 461 GLN Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 660 ILE 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: 1.9990 chunk 83 optimal weight: 0.0370 chunk 68 optimal weight: 7.9990 chunk 27 optimal weight: 0.0000 chunk 100 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 89 optimal weight: 0.0980 chunk 99 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 80 optimal weight: 6.9990 overall best weight: 0.2662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8828 Z= 0.152 Angle : 0.510 7.699 11978 Z= 0.248 Chirality : 0.039 0.219 1434 Planarity : 0.004 0.038 1458 Dihedral : 5.721 57.592 1338 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.42 % Allowed : 24.04 % Favored : 72.54 % 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: 1.64 (0.27), residues: 1086 helix: 1.83 (0.20), residues: 694 sheet: -2.02 (0.63), residues: 58 loop : 0.23 (0.39), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 575 HIS 0.004 0.001 HIS B 154 PHE 0.038 0.001 PHE A 275 TYR 0.009 0.001 TYR A 526 ARG 0.002 0.000 ARG A 436 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 146 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7832 (mmmt) cc_final: 0.7606 (mmmt) REVERT: A 256 LYS cc_start: 0.8266 (mmtt) cc_final: 0.7978 (mmmm) REVERT: A 508 TYR cc_start: 0.7402 (m-10) cc_final: 0.6509 (t80) REVERT: B 630 ILE cc_start: 0.7967 (mp) cc_final: 0.7659 (mp) REVERT: B 636 TRP cc_start: 0.8114 (m100) cc_final: 0.7707 (m100) outliers start: 32 outliers final: 21 residues processed: 161 average time/residue: 0.2041 time to fit residues: 45.9981 Evaluate side-chains 154 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 133 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 GLN B 154 HIS ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8828 Z= 0.298 Angle : 0.572 7.729 11978 Z= 0.278 Chirality : 0.041 0.219 1434 Planarity : 0.004 0.040 1458 Dihedral : 5.869 55.710 1338 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.38 % Allowed : 23.08 % Favored : 72.54 % 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: 1.35 (0.26), residues: 1086 helix: 1.53 (0.19), residues: 694 sheet: -1.74 (0.71), residues: 48 loop : 0.14 (0.38), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 447 HIS 0.005 0.001 HIS B 219 PHE 0.035 0.002 PHE A 275 TYR 0.012 0.002 TYR A 526 ARG 0.003 0.000 ARG A 401 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 138 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 LYS cc_start: 0.8353 (mmtt) cc_final: 0.8034 (mmmm) REVERT: B 274 MET cc_start: 0.8002 (mmm) cc_final: 0.7308 (mmt) REVERT: B 291 LYS cc_start: 0.8315 (ttmm) cc_final: 0.7850 (ttpt) REVERT: B 517 LEU cc_start: 0.8481 (mm) cc_final: 0.8263 (mm) REVERT: B 630 ILE cc_start: 0.8045 (mp) cc_final: 0.7701 (mp) REVERT: B 636 TRP cc_start: 0.8168 (m100) cc_final: 0.7779 (m100) outliers start: 41 outliers final: 28 residues processed: 163 average time/residue: 0.2038 time to fit residues: 46.7426 Evaluate side-chains 162 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 134 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 GLN B 154 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8828 Z= 0.250 Angle : 0.546 7.767 11978 Z= 0.266 Chirality : 0.040 0.220 1434 Planarity : 0.004 0.040 1458 Dihedral : 5.774 55.593 1338 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.59 % Allowed : 23.93 % Favored : 71.47 % 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: 1.42 (0.26), residues: 1086 helix: 1.58 (0.19), residues: 694 sheet: -1.68 (0.71), residues: 48 loop : 0.17 (0.38), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 575 HIS 0.005 0.001 HIS B 219 PHE 0.047 0.002 PHE A 275 TYR 0.011 0.001 TYR B 526 ARG 0.002 0.000 ARG A 436 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 145 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7846 (mmmt) cc_final: 0.7529 (mmmt) REVERT: A 256 LYS cc_start: 0.8326 (mmtt) cc_final: 0.8010 (mmmm) REVERT: A 508 TYR cc_start: 0.7292 (m-10) cc_final: 0.6173 (t80) REVERT: B 291 LYS cc_start: 0.8301 (ttmm) cc_final: 0.7832 (ttpt) REVERT: B 517 LEU cc_start: 0.8393 (mm) cc_final: 0.8167 (mm) REVERT: B 630 ILE cc_start: 0.8071 (mp) cc_final: 0.7758 (mp) REVERT: B 636 TRP cc_start: 0.8229 (m100) cc_final: 0.7861 (m100) outliers start: 43 outliers final: 36 residues processed: 171 average time/residue: 0.1916 time to fit residues: 46.4832 Evaluate side-chains 172 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 136 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.3980 chunk 95 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 106 optimal weight: 0.0870 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 GLN B 154 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8828 Z= 0.237 Angle : 0.543 7.835 11978 Z= 0.263 Chirality : 0.040 0.213 1434 Planarity : 0.004 0.041 1458 Dihedral : 5.718 55.324 1338 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.91 % Allowed : 24.04 % Favored : 71.05 % 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: 1.46 (0.26), residues: 1086 helix: 1.58 (0.19), residues: 698 sheet: -1.60 (0.72), residues: 48 loop : 0.24 (0.39), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 575 HIS 0.004 0.001 HIS B 219 PHE 0.041 0.002 PHE A 275 TYR 0.011 0.001 TYR B 526 ARG 0.002 0.000 ARG A 436 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 139 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7790 (mmmt) cc_final: 0.7509 (mmmt) REVERT: A 256 LYS cc_start: 0.8315 (mmtt) cc_final: 0.7991 (mmmm) REVERT: A 508 TYR cc_start: 0.7250 (m-10) cc_final: 0.6175 (t80) REVERT: B 291 LYS cc_start: 0.8301 (ttmm) cc_final: 0.7843 (ttpt) REVERT: B 517 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8140 (mm) REVERT: B 630 ILE cc_start: 0.8064 (mp) cc_final: 0.7756 (mp) REVERT: B 636 TRP cc_start: 0.8241 (m100) cc_final: 0.7907 (m100) outliers start: 46 outliers final: 37 residues processed: 170 average time/residue: 0.1889 time to fit residues: 45.4497 Evaluate side-chains 174 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 136 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 89 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 106 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 GLN B 154 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8828 Z= 0.222 Angle : 0.533 7.028 11978 Z= 0.258 Chirality : 0.040 0.213 1434 Planarity : 0.004 0.041 1458 Dihedral : 5.656 55.593 1338 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.81 % Allowed : 24.15 % Favored : 71.05 % 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: 1.52 (0.26), residues: 1086 helix: 1.64 (0.19), residues: 698 sheet: -1.56 (0.72), residues: 48 loop : 0.24 (0.39), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 575 HIS 0.004 0.001 HIS B 219 PHE 0.036 0.001 PHE A 275 TYR 0.011 0.001 TYR A 526 ARG 0.002 0.000 ARG B 650 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 137 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7779 (mmmt) cc_final: 0.7533 (mmmt) REVERT: A 256 LYS cc_start: 0.8283 (mmtt) cc_final: 0.7970 (mmmm) REVERT: A 508 TYR cc_start: 0.7271 (m-10) cc_final: 0.6292 (t80) REVERT: B 291 LYS cc_start: 0.8315 (ttmm) cc_final: 0.7856 (ttpt) REVERT: B 517 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8160 (mm) REVERT: B 630 ILE cc_start: 0.8061 (mp) cc_final: 0.7745 (mp) REVERT: B 636 TRP cc_start: 0.8206 (m100) cc_final: 0.7887 (m100) outliers start: 45 outliers final: 40 residues processed: 166 average time/residue: 0.1964 time to fit residues: 45.9873 Evaluate side-chains 172 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 131 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 461 GLN Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 0.1980 chunk 67 optimal weight: 0.9990 chunk 72 optimal weight: 0.0870 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 HIS ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8828 Z= 0.174 Angle : 0.519 7.123 11978 Z= 0.251 Chirality : 0.039 0.208 1434 Planarity : 0.004 0.041 1458 Dihedral : 5.501 55.002 1338 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.95 % Allowed : 24.79 % Favored : 71.26 % 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: 1.76 (0.27), residues: 1086 helix: 1.84 (0.20), residues: 694 sheet: -1.43 (0.73), residues: 48 loop : 0.31 (0.39), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 575 HIS 0.004 0.001 HIS A 154 PHE 0.033 0.001 PHE A 275 TYR 0.010 0.001 TYR A 526 ARG 0.005 0.000 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 141 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7765 (mmmt) cc_final: 0.7195 (mmmt) REVERT: A 136 LYS cc_start: 0.7468 (OUTLIER) cc_final: 0.7061 (mmtm) REVERT: A 256 LYS cc_start: 0.8287 (mmtt) cc_final: 0.7973 (mmmm) REVERT: A 508 TYR cc_start: 0.7138 (m-10) cc_final: 0.6320 (t80) REVERT: B 90 MET cc_start: 0.7588 (ptt) cc_final: 0.7335 (ptt) REVERT: B 291 LYS cc_start: 0.8335 (ttmm) cc_final: 0.7867 (ttpt) REVERT: B 517 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8139 (mm) REVERT: B 630 ILE cc_start: 0.8035 (mp) cc_final: 0.7719 (mp) REVERT: B 636 TRP cc_start: 0.8208 (m100) cc_final: 0.7864 (m100) outliers start: 37 outliers final: 27 residues processed: 166 average time/residue: 0.1950 time to fit residues: 45.8470 Evaluate side-chains 163 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 655 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 77 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 GLN ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8828 Z= 0.308 Angle : 0.591 8.099 11978 Z= 0.286 Chirality : 0.042 0.219 1434 Planarity : 0.004 0.060 1458 Dihedral : 5.651 56.246 1336 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.38 % Allowed : 24.36 % Favored : 71.26 % 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: 1.45 (0.26), residues: 1086 helix: 1.56 (0.19), residues: 692 sheet: -1.86 (0.63), residues: 68 loop : 0.52 (0.40), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 575 HIS 0.006 0.001 HIS B 154 PHE 0.037 0.002 PHE A 275 TYR 0.012 0.002 TYR B 526 ARG 0.006 0.000 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 137 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7775 (mmmt) cc_final: 0.7216 (mmmt) REVERT: A 256 LYS cc_start: 0.8354 (mmtt) cc_final: 0.7982 (mmmm) REVERT: B 291 LYS cc_start: 0.8396 (ttmm) cc_final: 0.7952 (ttpt) REVERT: B 517 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8189 (mm) REVERT: B 630 ILE cc_start: 0.8084 (mp) cc_final: 0.7738 (mp) REVERT: B 636 TRP cc_start: 0.8250 (m100) cc_final: 0.7895 (m100) outliers start: 41 outliers final: 37 residues processed: 163 average time/residue: 0.1930 time to fit residues: 44.2629 Evaluate side-chains 175 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 137 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 461 GLN Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 256 LYS Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.2980 chunk 72 optimal weight: 0.0980 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 GLN ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8828 Z= 0.179 Angle : 0.534 7.749 11978 Z= 0.258 Chirality : 0.039 0.208 1434 Planarity : 0.004 0.047 1458 Dihedral : 5.443 55.986 1336 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.95 % Allowed : 24.68 % Favored : 71.37 % 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: 1.74 (0.27), residues: 1086 helix: 1.85 (0.20), residues: 690 sheet: -1.83 (0.63), residues: 68 loop : 0.48 (0.40), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 575 HIS 0.005 0.001 HIS B 154 PHE 0.036 0.001 PHE A 275 TYR 0.009 0.001 TYR A 526 ARG 0.008 0.000 ARG B 401 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 141 time to evaluate : 1.121 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7806 (mmmt) cc_final: 0.7226 (mmmt) REVERT: A 136 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.7021 (mmtm) REVERT: A 256 LYS cc_start: 0.8297 (mmtt) cc_final: 0.7937 (mmmm) REVERT: A 517 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7701 (mp) REVERT: B 291 LYS cc_start: 0.8315 (ttmm) cc_final: 0.7860 (ttpt) REVERT: B 304 PHE cc_start: 0.7788 (m-80) cc_final: 0.7527 (m-80) REVERT: B 468 ARG cc_start: 0.8030 (tpp80) cc_final: 0.7829 (ttm170) REVERT: B 517 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8152 (mm) REVERT: B 630 ILE cc_start: 0.8005 (mp) cc_final: 0.7687 (mp) REVERT: B 636 TRP cc_start: 0.8212 (m100) cc_final: 0.7895 (m100) outliers start: 37 outliers final: 33 residues processed: 164 average time/residue: 0.2038 time to fit residues: 46.8024 Evaluate side-chains 173 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 137 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 461 GLN Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 655 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.166715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.123219 restraints weight = 9444.020| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.99 r_work: 0.3238 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8828 Z= 0.220 Angle : 0.546 7.873 11978 Z= 0.264 Chirality : 0.040 0.211 1434 Planarity : 0.004 0.057 1458 Dihedral : 5.488 56.501 1336 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.38 % Allowed : 24.36 % Favored : 71.26 % 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: 1.68 (0.27), residues: 1086 helix: 1.72 (0.19), residues: 698 sheet: -1.80 (0.63), residues: 68 loop : 0.63 (0.41), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 575 HIS 0.006 0.001 HIS B 154 PHE 0.038 0.001 PHE A 275 TYR 0.011 0.001 TYR A 526 ARG 0.006 0.000 ARG B 401 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2091.23 seconds wall clock time: 38 minutes 41.48 seconds (2321.48 seconds total)