Starting phenix.real_space_refine on Fri Dec 8 15:11:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wba_37418/12_2023/8wba_37418.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wba_37418/12_2023/8wba_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_37418/12_2023/8wba_37418.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wba_37418/12_2023/8wba_37418.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wba_37418/12_2023/8wba_37418.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wba_37418/12_2023/8wba_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-1.21rc1-5172/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: 5.13, per 1000 atoms: 0.59 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: 3.54 Conformation dependent library (CDL) restraints added in 1.7 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: 1.05 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: 2.40 Time building geometry restraints manager: 3.83 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: 1.230 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: 4.100 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 26.470 Find NCS groups from input model: 0.500 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.590 ------------------------------------------------------------------------------- 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 : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 131 average time/residue: 0.2047 time to fit residues: 37.6455 Evaluate side-chains 128 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 0.837 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0794 time to fit residues: 1.5825 ------------------------------------------------------------------------------- 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: 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 413 GLN A 461 GLN B 531 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8828 Z= 0.322 Angle : 0.594 8.966 11978 Z= 0.289 Chirality : 0.042 0.230 1434 Planarity : 0.005 0.045 1458 Dihedral : 5.749 59.761 1336 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.70 % Allowed : 21.69 % Favored : 73.61 % 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: 1.22 (0.26), residues: 1086 helix: 1.44 (0.19), residues: 696 sheet: -2.14 (0.62), residues: 58 loop : 0.21 (0.39), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 447 HIS 0.006 0.001 HIS A 219 PHE 0.031 0.002 PHE A 275 TYR 0.013 0.002 TYR A 526 ARG 0.003 0.000 ARG A 510 *********************** 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 186 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 142 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 24 residues processed: 171 average time/residue: 0.1912 time to fit residues: 46.7700 Evaluate side-chains 159 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 135 time to evaluate : 1.150 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.0828 time to fit residues: 5.0724 ------------------------------------------------------------------------------- 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: 1.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 27 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 89 optimal weight: 0.0980 chunk 99 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 GLN ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8828 Z= 0.241 Angle : 0.555 7.939 11978 Z= 0.271 Chirality : 0.041 0.220 1434 Planarity : 0.004 0.040 1458 Dihedral : 5.586 57.531 1336 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.71 % Allowed : 24.79 % 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: 1.35 (0.26), residues: 1086 helix: 1.55 (0.19), residues: 694 sheet: -2.14 (0.62), residues: 58 loop : 0.27 (0.39), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 575 HIS 0.005 0.001 HIS B 154 PHE 0.045 0.002 PHE A 275 TYR 0.011 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 159 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 143 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 4 residues processed: 153 average time/residue: 0.2067 time to fit residues: 44.2060 Evaluate side-chains 138 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 134 time to evaluate : 0.881 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0875 time to fit residues: 2.0037 ------------------------------------------------------------------------------- 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: 1.9990 chunk 51 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8828 Z= 0.334 Angle : 0.591 7.781 11978 Z= 0.288 Chirality : 0.042 0.223 1434 Planarity : 0.004 0.041 1458 Dihedral : 5.775 56.106 1336 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.53 % Allowed : 24.04 % Favored : 72.44 % 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: 1.13 (0.26), residues: 1086 helix: 1.36 (0.19), residues: 694 sheet: -1.98 (0.70), residues: 48 loop : 0.10 (0.38), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 575 HIS 0.005 0.001 HIS B 219 PHE 0.037 0.002 PHE B 275 TYR 0.012 0.002 TYR A 526 ARG 0.003 0.000 ARG A 410 *********************** 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 172 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 139 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 19 residues processed: 158 average time/residue: 0.2015 time to fit residues: 45.0593 Evaluate side-chains 154 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 135 time to evaluate : 0.856 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.0846 time to fit residues: 4.3047 ------------------------------------------------------------------------------- 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: 0.9980 chunk 60 optimal weight: 0.0670 chunk 1 optimal weight: 8.9990 chunk 79 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8828 Z= 0.207 Angle : 0.544 7.596 11978 Z= 0.266 Chirality : 0.041 0.246 1434 Planarity : 0.004 0.039 1458 Dihedral : 5.562 55.324 1336 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.39 % Allowed : 26.50 % Favored : 72.12 % 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: 1.38 (0.26), residues: 1086 helix: 1.59 (0.19), residues: 694 sheet: -1.93 (0.70), residues: 48 loop : 0.08 (0.38), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 575 HIS 0.004 0.001 HIS B 154 PHE 0.042 0.002 PHE A 275 TYR 0.010 0.001 TYR A 526 ARG 0.006 0.000 ARG A 338 *********************** 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 160 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 147 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 156 average time/residue: 0.2005 time to fit residues: 43.9250 Evaluate side-chains 146 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 140 time to evaluate : 0.917 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0841 time to fit residues: 2.1468 ------------------------------------------------------------------------------- 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: 0.6980 chunk 95 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 62 optimal weight: 0.3980 chunk 26 optimal weight: 0.6980 chunk 106 optimal weight: 8.9990 chunk 88 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1488 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= 0.218 Angle : 0.544 7.829 11978 Z= 0.265 Chirality : 0.040 0.211 1434 Planarity : 0.004 0.041 1458 Dihedral : 5.501 54.571 1336 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.50 % Allowed : 26.71 % Favored : 71.79 % 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: 1.60 (0.19), residues: 698 sheet: -1.98 (0.70), residues: 48 loop : 0.16 (0.39), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 575 HIS 0.004 0.001 HIS B 154 PHE 0.041 0.002 PHE A 275 TYR 0.010 0.001 TYR B 526 ARG 0.003 0.000 ARG A 338 *********************** 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 148 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 134 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 139 average time/residue: 0.2169 time to fit residues: 42.0729 Evaluate side-chains 142 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 132 time to evaluate : 0.860 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0849 time to fit residues: 2.9614 ------------------------------------------------------------------------------- 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: 2.9990 chunk 60 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 106 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8828 Z= 0.236 Angle : 0.551 7.154 11978 Z= 0.268 Chirality : 0.041 0.210 1434 Planarity : 0.004 0.041 1458 Dihedral : 5.510 55.525 1336 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.71 % Allowed : 26.07 % Favored : 72.22 % 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: 1.39 (0.26), residues: 1086 helix: 1.57 (0.19), residues: 698 sheet: -1.97 (0.69), residues: 48 loop : 0.15 (0.39), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 575 HIS 0.006 0.001 HIS B 484 PHE 0.035 0.002 PHE A 275 TYR 0.010 0.001 TYR B 526 ARG 0.005 0.000 ARG B 401 *********************** 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 148 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 0.907 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 146 average time/residue: 0.2299 time to fit residues: 47.0000 Evaluate side-chains 137 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 131 time to evaluate : 1.056 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0940 time to fit residues: 2.4848 ------------------------------------------------------------------------------- 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: 0.6980 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 83 optimal weight: 0.3980 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.7817 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8828 Z= 0.232 Angle : 0.561 8.133 11978 Z= 0.272 Chirality : 0.041 0.271 1434 Planarity : 0.004 0.042 1458 Dihedral : 5.502 55.686 1336 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.50 % Allowed : 26.28 % Favored : 72.22 % 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: 1.47 (0.27), residues: 1086 helix: 1.64 (0.19), residues: 692 sheet: -2.20 (0.60), residues: 68 loop : 0.44 (0.40), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 575 HIS 0.004 0.001 HIS B 154 PHE 0.034 0.002 PHE A 275 TYR 0.010 0.001 TYR B 526 ARG 0.003 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 147 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 133 time to evaluate : 0.967 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 138 average time/residue: 0.2068 time to fit residues: 39.9695 Evaluate side-chains 139 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 130 time to evaluate : 0.928 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0835 time to fit residues: 2.7108 ------------------------------------------------------------------------------- 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: 0.5980 chunk 101 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 77 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7812 moved from start: 0.1630 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= 0.227 Angle : 0.563 8.547 11978 Z= 0.272 Chirality : 0.041 0.306 1434 Planarity : 0.004 0.042 1458 Dihedral : 5.498 56.183 1336 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.18 % Allowed : 25.96 % Favored : 72.86 % 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: 1.53 (0.27), residues: 1086 helix: 1.67 (0.19), residues: 690 sheet: -2.07 (0.61), residues: 68 loop : 0.48 (0.40), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 575 HIS 0.004 0.001 HIS B 154 PHE 0.035 0.002 PHE A 275 TYR 0.010 0.001 TYR A 526 ARG 0.002 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 143 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 132 time to evaluate : 1.022 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 140 average time/residue: 0.2048 time to fit residues: 40.5241 Evaluate side-chains 138 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 132 time to evaluate : 0.962 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0853 time to fit residues: 2.2962 ------------------------------------------------------------------------------- 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: 0.2980 chunk 72 optimal weight: 0.0980 chunk 109 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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: 0.7778 moved from start: 0.1579 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 : 0.546 8.200 11978 Z= 0.263 Chirality : 0.040 0.285 1434 Planarity : 0.004 0.043 1458 Dihedral : 5.407 56.290 1336 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.21 % Allowed : 26.92 % Favored : 72.86 % 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: 1.70 (0.27), residues: 1086 helix: 1.81 (0.20), residues: 696 sheet: -2.09 (0.61), residues: 68 loop : 0.53 (0.41), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 575 HIS 0.005 0.001 HIS B 154 PHE 0.034 0.001 PHE A 275 TYR 0.009 0.001 TYR A 526 ARG 0.002 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 143 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 141 time to evaluate : 0.913 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 141 average time/residue: 0.2126 time to fit residues: 41.7631 Evaluate side-chains 133 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 0.995 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0832 time to fit residues: 1.5556 ------------------------------------------------------------------------------- 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: 4.9990 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 HIS B 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.169842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.126694 restraints weight = 9360.982| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.05 r_work: 0.3228 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1699 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= 0.229 Angle : 0.570 8.284 11978 Z= 0.274 Chirality : 0.041 0.297 1434 Planarity : 0.004 0.062 1458 Dihedral : 5.481 56.822 1336 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.32 % Allowed : 27.56 % Favored : 72.12 % 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: 1.61 (0.27), residues: 1086 helix: 1.72 (0.20), residues: 698 sheet: -2.11 (0.61), residues: 68 loop : 0.56 (0.41), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 575 HIS 0.004 0.001 HIS A 154 PHE 0.039 0.002 PHE A 275 TYR 0.010 0.001 TYR A 526 ARG 0.002 0.000 ARG A 436 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2013.11 seconds wall clock time: 37 minutes 33.10 seconds (2253.10 seconds total)