Starting phenix.real_space_refine on Mon Mar 11 18:18:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1q_21015/03_2024/6v1q_21015.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1q_21015/03_2024/6v1q_21015.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1q_21015/03_2024/6v1q_21015.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1q_21015/03_2024/6v1q_21015.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1q_21015/03_2024/6v1q_21015.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1q_21015/03_2024/6v1q_21015.pdb" } resolution = 3.11 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= -0.001 sd= 0.082 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 38 5.16 5 Na 1 4.78 5 C 5920 2.51 5 N 1402 2.21 5 O 1464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 93": "OD1" <-> "OD2" Residue "A GLU 108": "OE1" <-> "OE2" Residue "A ARG 118": "NH1" <-> "NH2" Residue "A TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A ARG 224": "NH1" <-> "NH2" Residue "A TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 301": "OE1" <-> "OE2" Residue "A ASP 438": "OD1" <-> "OD2" Residue "A GLU 440": "OE1" <-> "OE2" Residue "A PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 583": "OD1" <-> "OD2" Residue "A PHE 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 93": "OD1" <-> "OD2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B ARG 224": "NH1" <-> "NH2" Residue "B TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 301": "OE1" <-> "OE2" Residue "B ASP 438": "OD1" <-> "OD2" Residue "B GLU 440": "OE1" <-> "OE2" Residue "B PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 583": "OD1" <-> "OD2" Residue "B PHE 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 668": "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: 8825 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4412 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 17, 'TRANS': 520} Chain breaks: 2 Chain: "B" Number of atoms: 4412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4412 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 17, 'TRANS': 520} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.15, per 1000 atoms: 0.58 Number of scatterers: 8825 At special positions: 0 Unit cell: (124.344, 116.808, 97.968, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 Na 1 11.00 O 1464 8.00 N 1402 7.00 C 5920 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.40 Conformation dependent library (CDL) restraints added in 1.7 seconds 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2080 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 0 sheets defined 70.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 36 through 46 Processing helix chain 'A' and resid 63 through 70 Processing helix chain 'A' and resid 71 through 88 removed outlier: 3.641A pdb=" N TYR A 79 " --> pdb=" O GLN A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 100 through 126 removed outlier: 3.696A pdb=" N ILE A 107 " --> pdb=" O ALA A 103 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU A 108 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE A 110 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 154 Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 171 through 179 removed outlier: 3.742A pdb=" N LEU A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU A 176 " --> pdb=" O ARG A 172 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 177 " --> pdb=" O PRO A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 220 removed outlier: 3.524A pdb=" N ARG A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA A 188 " --> pdb=" O GLN A 184 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE A 192 " --> pdb=" O ALA A 188 " (cutoff:3.500A) Proline residue: A 197 - end of helix removed outlier: 3.976A pdb=" N TYR A 201 " --> pdb=" O PRO A 197 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU A 205 " --> pdb=" O TYR A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 250 removed outlier: 3.732A pdb=" N PHE A 243 " --> pdb=" O MET A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 268 through 279 removed outlier: 3.836A pdb=" N PHE A 272 " --> pdb=" O PHE A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 300 removed outlier: 3.812A pdb=" N LEU A 288 " --> pdb=" O MET A 284 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS A 300 " --> pdb=" O LYS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 320 removed outlier: 4.862A pdb=" N LYS A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N PHE A 318 " --> pdb=" O MET A 314 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER A 319 " --> pdb=" O CYS A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 415 Processing helix chain 'A' and resid 420 through 432 Processing helix chain 'A' and resid 441 through 457 removed outlier: 3.709A pdb=" N ALA A 447 " --> pdb=" O VAL A 443 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N TRP A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY A 450 " --> pdb=" O ASN A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 490 removed outlier: 3.544A pdb=" N THR A 483 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 484 " --> pdb=" O TRP A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 500 removed outlier: 3.786A pdb=" N ILE A 495 " --> pdb=" O PHE A 491 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS A 500 " --> pdb=" O ASN A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 522 removed outlier: 4.096A pdb=" N ILE A 516 " --> pdb=" O ASP A 512 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU A 520 " --> pdb=" O ILE A 516 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU A 522 " --> pdb=" O ARG A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 530 Processing helix chain 'A' and resid 543 through 568 removed outlier: 4.197A pdb=" N LEU A 547 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU A 554 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 567 " --> pdb=" O VAL A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 584 Processing helix chain 'A' and resid 589 through 593 Processing helix chain 'A' and resid 609 through 622 removed outlier: 3.602A pdb=" N LEU A 616 " --> pdb=" O SER A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 634 removed outlier: 3.504A pdb=" N PHE A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 641 through 653 removed outlier: 3.820A pdb=" N PHE A 645 " --> pdb=" O ALA A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 670 removed outlier: 3.704A pdb=" N PHE A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE A 668 " --> pdb=" O ILE A 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 46 Processing helix chain 'B' and resid 63 through 70 Processing helix chain 'B' and resid 71 through 88 removed outlier: 3.641A pdb=" N TYR B 79 " --> pdb=" O GLN B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 100 through 126 removed outlier: 3.697A pdb=" N ILE B 107 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU B 108 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 154 Processing helix chain 'B' and resid 168 through 170 No H-bonds generated for 'chain 'B' and resid 168 through 170' Processing helix chain 'B' and resid 171 through 179 removed outlier: 3.742A pdb=" N LEU B 175 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU B 176 " --> pdb=" O ARG B 172 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL B 177 " --> pdb=" O PRO B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 220 removed outlier: 3.524A pdb=" N ARG B 187 " --> pdb=" O ARG B 183 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA B 188 " --> pdb=" O GLN B 184 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE B 192 " --> pdb=" O ALA B 188 " (cutoff:3.500A) Proline residue: B 197 - end of helix removed outlier: 3.976A pdb=" N TYR B 201 " --> pdb=" O PRO B 197 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU B 205 " --> pdb=" O TYR B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 250 removed outlier: 3.733A pdb=" N PHE B 243 " --> pdb=" O MET B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 268 through 279 removed outlier: 3.835A pdb=" N PHE B 272 " --> pdb=" O PHE B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 300 removed outlier: 3.813A pdb=" N LEU B 288 " --> pdb=" O MET B 284 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS B 300 " --> pdb=" O LYS B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 320 removed outlier: 4.861A pdb=" N LYS B 313 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N PHE B 318 " --> pdb=" O MET B 314 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER B 319 " --> pdb=" O CYS B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 415 Processing helix chain 'B' and resid 420 through 432 Processing helix chain 'B' and resid 441 through 457 removed outlier: 3.709A pdb=" N ALA B 447 " --> pdb=" O VAL B 443 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N TRP B 449 " --> pdb=" O SER B 445 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 450 " --> pdb=" O ASN B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 490 removed outlier: 3.544A pdb=" N THR B 483 " --> pdb=" O ASN B 479 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 484 " --> pdb=" O TRP B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 500 removed outlier: 3.787A pdb=" N ILE B 495 " --> pdb=" O PHE B 491 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS B 500 " --> pdb=" O ASN B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 522 removed outlier: 4.096A pdb=" N ILE B 516 " --> pdb=" O ASP B 512 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU B 517 " --> pdb=" O ILE B 513 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU B 520 " --> pdb=" O ILE B 516 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU B 522 " --> pdb=" O ARG B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 530 Processing helix chain 'B' and resid 543 through 568 removed outlier: 4.197A pdb=" N LEU B 547 " --> pdb=" O GLY B 543 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU B 554 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU B 566 " --> pdb=" O MET B 562 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 567 " --> pdb=" O VAL B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 584 Processing helix chain 'B' and resid 589 through 593 Processing helix chain 'B' and resid 609 through 622 removed outlier: 3.602A pdb=" N LEU B 616 " --> pdb=" O SER B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 634 removed outlier: 3.504A pdb=" N PHE B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 640 No H-bonds generated for 'chain 'B' and resid 638 through 640' Processing helix chain 'B' and resid 641 through 653 removed outlier: 3.820A pdb=" N PHE B 645 " --> pdb=" O ALA B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 670 removed outlier: 3.704A pdb=" N PHE B 663 " --> pdb=" O ILE B 659 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE B 668 " --> pdb=" O ILE B 664 " (cutoff:3.500A) 452 hydrogen bonds defined for protein. 1302 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: 2.21 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1286 1.28 - 1.41: 2510 1.41 - 1.54: 5151 1.54 - 1.67: 43 1.67 - 1.81: 66 Bond restraints: 9056 Sorted by residual: bond pdb=" CA PRO A 135 " pdb=" C PRO A 135 " ideal model delta sigma weight residual 1.516 1.411 0.105 1.42e-02 4.96e+03 5.51e+01 bond pdb=" CA PRO B 135 " pdb=" C PRO B 135 " ideal model delta sigma weight residual 1.516 1.411 0.105 1.42e-02 4.96e+03 5.48e+01 bond pdb=" C ASP B 134 " pdb=" O ASP B 134 " ideal model delta sigma weight residual 1.237 1.142 0.095 1.29e-02 6.01e+03 5.43e+01 bond pdb=" C ASP A 134 " pdb=" O ASP A 134 " ideal model delta sigma weight residual 1.237 1.143 0.095 1.29e-02 6.01e+03 5.37e+01 bond pdb=" N LYS B 133 " pdb=" CA LYS B 133 " ideal model delta sigma weight residual 1.456 1.364 0.093 1.33e-02 5.65e+03 4.85e+01 ... (remaining 9051 not shown) Histogram of bond angle deviations from ideal: 95.71 - 103.69: 104 103.69 - 111.66: 4180 111.66 - 119.64: 3581 119.64 - 127.62: 4363 127.62 - 135.59: 82 Bond angle restraints: 12310 Sorted by residual: angle pdb=" C ILE A 459 " pdb=" N LEU A 460 " pdb=" CA LEU A 460 " ideal model delta sigma weight residual 121.83 135.59 -13.76 1.48e+00 4.57e-01 8.64e+01 angle pdb=" C ILE B 459 " pdb=" N LEU B 460 " pdb=" CA LEU B 460 " ideal model delta sigma weight residual 121.83 135.58 -13.75 1.48e+00 4.57e-01 8.63e+01 angle pdb=" N TYR B 262 " pdb=" CA TYR B 262 " pdb=" C TYR B 262 " ideal model delta sigma weight residual 114.75 105.22 9.53 1.26e+00 6.30e-01 5.72e+01 angle pdb=" N TYR A 262 " pdb=" CA TYR A 262 " pdb=" C TYR A 262 " ideal model delta sigma weight residual 114.75 105.25 9.50 1.26e+00 6.30e-01 5.68e+01 angle pdb=" CA ILE B 459 " pdb=" C ILE B 459 " pdb=" N LEU B 460 " ideal model delta sigma weight residual 116.60 105.71 10.89 1.45e+00 4.76e-01 5.64e+01 ... (remaining 12305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 4513 17.64 - 35.29: 577 35.29 - 52.93: 152 52.93 - 70.57: 26 70.57 - 88.22: 10 Dihedral angle restraints: 5278 sinusoidal: 2072 harmonic: 3206 Sorted by residual: dihedral pdb=" CA LYS A 541 " pdb=" C LYS A 541 " pdb=" N ILE A 542 " pdb=" CA ILE A 542 " ideal model delta harmonic sigma weight residual -180.00 -131.46 -48.54 0 5.00e+00 4.00e-02 9.42e+01 dihedral pdb=" CA LYS B 541 " pdb=" C LYS B 541 " pdb=" N ILE B 542 " pdb=" CA ILE B 542 " ideal model delta harmonic sigma weight residual -180.00 -131.50 -48.50 0 5.00e+00 4.00e-02 9.41e+01 dihedral pdb=" C LEU A 457 " pdb=" N LEU A 457 " pdb=" CA LEU A 457 " pdb=" CB LEU A 457 " ideal model delta harmonic sigma weight residual -122.60 -143.97 21.37 0 2.50e+00 1.60e-01 7.31e+01 ... (remaining 5275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.179: 1438 0.179 - 0.357: 6 0.357 - 0.536: 2 0.536 - 0.715: 2 0.715 - 0.893: 4 Chirality restraints: 1452 Sorted by residual: chirality pdb=" CG LEU B 461 " pdb=" CB LEU B 461 " pdb=" CD1 LEU B 461 " pdb=" CD2 LEU B 461 " both_signs ideal model delta sigma weight residual False -2.59 -1.70 -0.89 2.00e-01 2.50e+01 1.99e+01 chirality pdb=" CG LEU A 461 " pdb=" CB LEU A 461 " pdb=" CD1 LEU A 461 " pdb=" CD2 LEU A 461 " both_signs ideal model delta sigma weight residual False -2.59 -1.70 -0.89 2.00e-01 2.50e+01 1.99e+01 chirality pdb=" CA LEU A 457 " pdb=" N LEU A 457 " pdb=" C LEU A 457 " pdb=" CB LEU A 457 " both_signs ideal model delta sigma weight residual False 2.51 1.64 0.87 2.00e-01 2.50e+01 1.91e+01 ... (remaining 1449 not shown) Planarity restraints: 1482 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 224 " 1.051 9.50e-02 1.11e+02 4.71e-01 1.34e+02 pdb=" NE ARG A 224 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG A 224 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 224 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 224 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 224 " -1.051 9.50e-02 1.11e+02 4.71e-01 1.34e+02 pdb=" NE ARG B 224 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG B 224 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 224 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 224 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 456 " -0.038 2.00e-02 2.50e+03 7.23e-02 5.22e+01 pdb=" C MET A 456 " 0.125 2.00e-02 2.50e+03 pdb=" O MET A 456 " -0.046 2.00e-02 2.50e+03 pdb=" N LEU A 457 " -0.041 2.00e-02 2.50e+03 ... (remaining 1479 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.10: 10 2.10 - 2.80: 2776 2.80 - 3.50: 12517 3.50 - 4.20: 21187 4.20 - 4.90: 36947 Nonbonded interactions: 73437 Sorted by model distance: nonbonded pdb=" NH2 ARG A 224 " pdb=" OE1 GLU B 440 " model vdw 1.396 2.520 nonbonded pdb=" OE1 GLU A 440 " pdb=" NH2 ARG B 224 " model vdw 1.396 2.520 nonbonded pdb=" NZ LYS A 219 " pdb=" OD2 ASP B 438 " model vdw 1.777 2.520 nonbonded pdb=" OD2 ASP A 438 " pdb=" NZ LYS B 219 " model vdw 1.786 2.520 nonbonded pdb=" NZ LYS A 223 " pdb=" OE2 GLU B 439 " model vdw 1.852 2.520 ... (remaining 73432 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 34 through 672) 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: 1.540 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: 4.940 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 25.610 Find NCS groups from input model: 0.490 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: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 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 : 0.008 0.105 9056 Z= 0.534 Angle : 1.007 14.986 12310 Z= 0.596 Chirality : 0.073 0.893 1452 Planarity : 0.018 0.471 1482 Dihedral : 17.131 88.216 3198 Min Nonbonded Distance : 1.396 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.40 % Favored : 90.23 % Rotamer: Outliers : 7.48 % Allowed : 18.14 % Favored : 74.39 % Cbeta Deviations : 0.58 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -4.86 (0.21), residues: 1064 helix: -2.97 (0.15), residues: 686 sheet: None (None), residues: 0 loop : -3.44 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 626 HIS 0.003 0.001 HIS B 121 PHE 0.010 0.001 PHE B 420 TYR 0.015 0.002 TYR B 163 ARG 0.004 0.000 ARG B 531 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 77 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LYS cc_start: 0.6204 (OUTLIER) cc_final: 0.5619 (ttmt) REVERT: A 441 ASN cc_start: 0.8936 (OUTLIER) cc_final: 0.8610 (p0) REVERT: A 541 LYS cc_start: 0.2714 (OUTLIER) cc_final: 0.2039 (mmtt) REVERT: A 546 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8202 (tp) REVERT: B 223 LYS cc_start: 0.6211 (OUTLIER) cc_final: 0.5662 (ttmt) REVERT: B 441 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8481 (p0) REVERT: B 541 LYS cc_start: 0.2774 (OUTLIER) cc_final: 0.2056 (mmtt) REVERT: B 546 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8294 (tp) outliers start: 73 outliers final: 35 residues processed: 146 average time/residue: 0.1968 time to fit residues: 40.0181 Evaluate side-chains 100 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 57 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 441 ASN Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 532 PHE Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 223 LYS Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 441 ASN Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 532 PHE Chi-restraints excluded: chain B residue 541 LYS Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 587 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 42 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 263 ASN A 279 ASN A 649 HIS A 658 ASN B 70 ASN B 194 ASN B 279 ASN B 649 HIS B 658 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9056 Z= 0.176 Angle : 0.683 10.854 12310 Z= 0.356 Chirality : 0.044 0.150 1452 Planarity : 0.004 0.033 1482 Dihedral : 9.594 58.274 1274 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.61 % Favored : 92.20 % Rotamer: Outliers : 5.53 % Allowed : 21.93 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.24), residues: 1064 helix: -1.36 (0.19), residues: 686 sheet: None (None), residues: 0 loop : -3.02 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 478 HIS 0.003 0.001 HIS B 71 PHE 0.021 0.001 PHE A 560 TYR 0.014 0.001 TYR B 455 ARG 0.002 0.000 ARG A 409 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 69 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 70 ASN cc_start: 0.7364 (OUTLIER) cc_final: 0.7150 (t0) REVERT: B 461 LEU cc_start: 0.5297 (OUTLIER) cc_final: 0.4422 (tp) outliers start: 54 outliers final: 18 residues processed: 117 average time/residue: 0.1963 time to fit residues: 33.0519 Evaluate side-chains 79 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 59 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain B residue 664 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 80 optimal weight: 0.4980 chunk 65 optimal weight: 0.0000 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 85 optimal weight: 9.9990 chunk 95 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9056 Z= 0.163 Angle : 0.642 7.340 12310 Z= 0.335 Chirality : 0.042 0.164 1452 Planarity : 0.003 0.023 1482 Dihedral : 6.922 53.781 1198 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.33 % Favored : 92.48 % Rotamer: Outliers : 4.00 % Allowed : 22.95 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.26), residues: 1064 helix: -0.76 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -2.89 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 478 HIS 0.005 0.001 HIS B 71 PHE 0.020 0.001 PHE A 477 TYR 0.015 0.001 TYR A 424 ARG 0.005 0.000 ARG A 418 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 59 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 ASN cc_start: 0.7351 (OUTLIER) cc_final: 0.7126 (t0) outliers start: 39 outliers final: 18 residues processed: 91 average time/residue: 0.1823 time to fit residues: 24.8156 Evaluate side-chains 72 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 53 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 664 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 70 ASN B 263 ASN B 625 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9056 Z= 0.163 Angle : 0.618 7.415 12310 Z= 0.321 Chirality : 0.043 0.260 1452 Planarity : 0.003 0.022 1482 Dihedral : 6.203 45.293 1180 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.79 % Allowed : 22.95 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.26), residues: 1064 helix: -0.38 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -2.74 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 626 HIS 0.005 0.001 HIS A 71 PHE 0.015 0.001 PHE A 560 TYR 0.020 0.001 TYR B 201 ARG 0.003 0.000 ARG B 531 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 62 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 LEU cc_start: 0.5364 (OUTLIER) cc_final: 0.5016 (tp) REVERT: B 70 ASN cc_start: 0.7452 (OUTLIER) cc_final: 0.7191 (t0) REVERT: B 461 LEU cc_start: 0.5498 (OUTLIER) cc_final: 0.5264 (tt) outliers start: 37 outliers final: 18 residues processed: 92 average time/residue: 0.1628 time to fit residues: 22.7709 Evaluate side-chains 77 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 56 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 664 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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: 0.7767 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9056 Z= 0.235 Angle : 0.645 7.436 12310 Z= 0.337 Chirality : 0.043 0.178 1452 Planarity : 0.003 0.022 1482 Dihedral : 5.754 44.835 1176 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 3.59 % Allowed : 23.16 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 (0.26), residues: 1064 helix: -0.18 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -2.66 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 626 HIS 0.005 0.001 HIS B 71 PHE 0.012 0.001 PHE A 560 TYR 0.020 0.001 TYR B 201 ARG 0.003 0.000 ARG A 531 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 58 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 LEU cc_start: 0.5781 (OUTLIER) cc_final: 0.5412 (tp) REVERT: A 562 MET cc_start: 0.7897 (mmp) cc_final: 0.7515 (mmp) REVERT: B 461 LEU cc_start: 0.5939 (OUTLIER) cc_final: 0.5560 (tp) REVERT: B 562 MET cc_start: 0.7875 (mmp) cc_final: 0.7585 (mmp) outliers start: 35 outliers final: 18 residues processed: 88 average time/residue: 0.1786 time to fit residues: 23.7139 Evaluate side-chains 72 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 52 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 664 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 98 optimal weight: 0.8980 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 70 ASN B 625 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9056 Z= 0.169 Angle : 0.619 7.909 12310 Z= 0.319 Chirality : 0.042 0.153 1452 Planarity : 0.003 0.022 1482 Dihedral : 5.606 43.249 1176 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.66 % Allowed : 24.69 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.44 (0.26), residues: 1064 helix: -0.07 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -2.69 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 626 HIS 0.002 0.001 HIS A 501 PHE 0.015 0.001 PHE A 560 TYR 0.014 0.001 TYR A 424 ARG 0.003 0.000 ARG A 531 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 64 time to evaluate : 1.049 Fit side-chains REVERT: A 461 LEU cc_start: 0.5446 (OUTLIER) cc_final: 0.5073 (tt) REVERT: B 461 LEU cc_start: 0.5583 (OUTLIER) cc_final: 0.5350 (tt) outliers start: 26 outliers final: 12 residues processed: 85 average time/residue: 0.1984 time to fit residues: 24.4107 Evaluate side-chains 64 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 50 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 664 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 47 optimal weight: 0.5980 chunk 40 optimal weight: 0.0980 chunk 61 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 70 ASN B 551 GLN B 625 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9056 Z= 0.154 Angle : 0.621 9.707 12310 Z= 0.316 Chirality : 0.041 0.137 1452 Planarity : 0.003 0.023 1482 Dihedral : 5.454 41.792 1176 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.77 % Allowed : 26.13 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.20 (0.27), residues: 1064 helix: 0.07 (0.20), residues: 698 sheet: None (None), residues: 0 loop : -2.49 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 626 HIS 0.002 0.001 HIS A 416 PHE 0.014 0.001 PHE B 560 TYR 0.013 0.001 TYR A 424 ARG 0.006 0.000 ARG B 518 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 63 time to evaluate : 1.106 Fit side-chains outliers start: 27 outliers final: 9 residues processed: 84 average time/residue: 0.1710 time to fit residues: 21.7939 Evaluate side-chains 64 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 664 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 0.0040 chunk 80 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 625 GLN B 70 ASN B 625 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9056 Z= 0.154 Angle : 0.634 10.354 12310 Z= 0.317 Chirality : 0.042 0.137 1452 Planarity : 0.003 0.035 1482 Dihedral : 5.358 40.432 1176 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 2.36 % Allowed : 26.64 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.15 (0.27), residues: 1064 helix: 0.16 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -2.60 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 626 HIS 0.002 0.000 HIS B 501 PHE 0.014 0.001 PHE B 560 TYR 0.012 0.001 TYR B 424 ARG 0.004 0.000 ARG B 518 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 64 time to evaluate : 1.061 Fit side-chains outliers start: 23 outliers final: 15 residues processed: 83 average time/residue: 0.1832 time to fit residues: 22.6567 Evaluate side-chains 72 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 57 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 664 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 70 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9056 Z= 0.279 Angle : 0.705 12.106 12310 Z= 0.355 Chirality : 0.044 0.160 1452 Planarity : 0.003 0.031 1482 Dihedral : 5.553 40.998 1176 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 1.95 % Allowed : 26.84 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.06 (0.27), residues: 1064 helix: 0.17 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -2.45 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 480 HIS 0.003 0.001 HIS B 417 PHE 0.012 0.001 PHE B 560 TYR 0.015 0.001 TYR A 424 ARG 0.004 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 53 time to evaluate : 0.962 Fit side-chains REVERT: B 562 MET cc_start: 0.7958 (mmp) cc_final: 0.7528 (mmp) outliers start: 19 outliers final: 15 residues processed: 68 average time/residue: 0.1735 time to fit residues: 18.6632 Evaluate side-chains 66 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 51 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 664 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 51 optimal weight: 0.0470 chunk 66 optimal weight: 0.0470 chunk 89 optimal weight: 0.9980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN ** B 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9056 Z= 0.146 Angle : 0.659 12.068 12310 Z= 0.323 Chirality : 0.042 0.137 1452 Planarity : 0.003 0.032 1482 Dihedral : 5.323 39.233 1176 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 1.54 % Allowed : 27.46 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.03 (0.27), residues: 1064 helix: 0.23 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -2.51 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 626 HIS 0.002 0.001 HIS A 121 PHE 0.013 0.001 PHE B 560 TYR 0.012 0.001 TYR B 424 ARG 0.004 0.000 ARG B 518 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 60 time to evaluate : 1.083 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 72 average time/residue: 0.1470 time to fit residues: 17.2508 Evaluate side-chains 69 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 664 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 84 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 70 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.066394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.057859 restraints weight = 45062.367| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.72 r_work: 0.3243 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9056 Z= 0.162 Angle : 0.652 11.421 12310 Z= 0.322 Chirality : 0.042 0.176 1452 Planarity : 0.003 0.023 1482 Dihedral : 5.234 38.716 1176 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 1.74 % Allowed : 27.56 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.98 (0.27), residues: 1064 helix: 0.27 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -2.48 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 626 HIS 0.002 0.001 HIS B 649 PHE 0.013 0.001 PHE A 560 TYR 0.013 0.001 TYR B 424 ARG 0.003 0.000 ARG B 518 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1735.61 seconds wall clock time: 32 minutes 34.36 seconds (1954.36 seconds total)