Starting phenix.real_space_refine on Sat Dec 9 00:51:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpf_6822/12_2023/6jpf_6822.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpf_6822/12_2023/6jpf_6822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpf_6822/12_2023/6jpf_6822.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpf_6822/12_2023/6jpf_6822.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpf_6822/12_2023/6jpf_6822.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpf_6822/12_2023/6jpf_6822.pdb" } resolution = 3.52 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= 0.003 sd= 0.071 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 42 5.16 5 C 6368 2.51 5 N 1572 2.21 5 O 1606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 36": "NH1" <-> "NH2" Residue "A ARG 45": "NH1" <-> "NH2" Residue "A PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 358": "NH1" <-> "NH2" Residue "A PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 36": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 358": "NH1" <-> "NH2" Residue "B PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 472": "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: 9588 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4794 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 32, 'TRANS': 577} Chain breaks: 6 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 4, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 90 Chain: "B" Number of atoms: 4794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4794 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 32, 'TRANS': 577} Chain breaks: 6 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 4, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 90 Time building chain proxies: 6.04, per 1000 atoms: 0.63 Number of scatterers: 9588 At special positions: 0 Unit cell: (119, 131, 91, 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 42 16.00 O 1606 8.00 N 1572 7.00 C 6368 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: 4.82 Conformation dependent library (CDL) restraints added in 2.1 seconds 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2340 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 4 sheets defined 75.5% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 4 through 31 Processing helix chain 'A' and resid 34 through 39 removed outlier: 3.605A pdb=" N TYR A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 75 through 81 removed outlier: 3.755A pdb=" N LEU A 80 " --> pdb=" O MET A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 118 removed outlier: 7.485A pdb=" N LEU A 93 " --> pdb=" O ASP A 89 " (cutoff:3.500A) removed outlier: 9.706A pdb=" N ASP A 94 " --> pdb=" O HIS A 90 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 157 through 195 removed outlier: 3.793A pdb=" N ILE A 164 " --> pdb=" O TRP A 160 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N MET A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 202 removed outlier: 3.743A pdb=" N PHE A 202 " --> pdb=" O ARG A 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 202' Processing helix chain 'A' and resid 216 through 229 Processing helix chain 'A' and resid 242 through 267 removed outlier: 3.660A pdb=" N TYR A 262 " --> pdb=" O TRP A 258 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N THR A 267 " --> pdb=" O GLN A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 314 Processing helix chain 'A' and resid 330 through 340 Processing helix chain 'A' and resid 361 through 365 Processing helix chain 'A' and resid 372 through 388 Processing helix chain 'A' and resid 390 through 402 removed outlier: 3.542A pdb=" N ILE A 394 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 439 removed outlier: 3.953A pdb=" N GLY A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 453 Processing helix chain 'A' and resid 457 through 476 removed outlier: 3.625A pdb=" N VAL A 475 " --> pdb=" O ILE A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 491 removed outlier: 3.769A pdb=" N GLN A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A 491 " --> pdb=" O ALA A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 524 removed outlier: 3.671A pdb=" N THR A 515 " --> pdb=" O PRO A 511 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE A 516 " --> pdb=" O MET A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 535 removed outlier: 4.012A pdb=" N LEU A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 548 Processing helix chain 'A' and resid 566 through 585 Proline residue: A 572 - end of helix Processing helix chain 'A' and resid 591 through 613 Processing helix chain 'A' and resid 624 through 648 removed outlier: 3.651A pdb=" N THR A 634 " --> pdb=" O GLY A 630 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY A 645 " --> pdb=" O LEU A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 682 removed outlier: 4.545A pdb=" N PHE A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) Proline residue: A 663 - end of helix Proline residue: A 679 - end of helix Processing helix chain 'A' and resid 685 through 700 Processing helix chain 'A' and resid 704 through 713 removed outlier: 4.386A pdb=" N TYR A 708 " --> pdb=" O ASN A 704 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR A 713 " --> pdb=" O LEU A 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 31 Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.606A pdb=" N TYR B 38 " --> pdb=" O ASN B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 75 through 81 removed outlier: 3.755A pdb=" N LEU B 80 " --> pdb=" O MET B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 118 removed outlier: 7.485A pdb=" N LEU B 93 " --> pdb=" O ASP B 89 " (cutoff:3.500A) removed outlier: 9.706A pdb=" N ASP B 94 " --> pdb=" O HIS B 90 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 157 through 195 removed outlier: 3.792A pdb=" N ILE B 164 " --> pdb=" O TRP B 160 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N MET B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 202 removed outlier: 3.744A pdb=" N PHE B 202 " --> pdb=" O ARG B 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 202' Processing helix chain 'B' and resid 216 through 229 Processing helix chain 'B' and resid 242 through 267 removed outlier: 3.659A pdb=" N TYR B 262 " --> pdb=" O TRP B 258 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N THR B 267 " --> pdb=" O GLN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 314 Processing helix chain 'B' and resid 330 through 340 Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 372 through 388 Processing helix chain 'B' and resid 390 through 402 removed outlier: 3.542A pdb=" N ILE B 394 " --> pdb=" O PHE B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 439 removed outlier: 3.952A pdb=" N GLY B 432 " --> pdb=" O GLY B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 453 Processing helix chain 'B' and resid 457 through 476 removed outlier: 3.626A pdb=" N VAL B 475 " --> pdb=" O ILE B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 491 removed outlier: 3.768A pdb=" N GLN B 490 " --> pdb=" O ALA B 486 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU B 491 " --> pdb=" O ALA B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 524 removed outlier: 3.672A pdb=" N THR B 515 " --> pdb=" O PRO B 511 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE B 516 " --> pdb=" O MET B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 535 removed outlier: 4.012A pdb=" N LEU B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 548 Processing helix chain 'B' and resid 566 through 585 Proline residue: B 572 - end of helix Processing helix chain 'B' and resid 591 through 613 Processing helix chain 'B' and resid 624 through 648 removed outlier: 3.651A pdb=" N THR B 634 " --> pdb=" O GLY B 630 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY B 645 " --> pdb=" O LEU B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 682 removed outlier: 4.546A pdb=" N PHE B 658 " --> pdb=" O SER B 654 " (cutoff:3.500A) Proline residue: B 663 - end of helix Proline residue: B 679 - end of helix Processing helix chain 'B' and resid 685 through 700 Processing helix chain 'B' and resid 704 through 713 removed outlier: 4.387A pdb=" N TYR B 708 " --> pdb=" O ASN B 704 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR B 713 " --> pdb=" O LEU B 709 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 235 removed outlier: 5.686A pdb=" N ALA A 323 " --> pdb=" O VAL A 239 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 233 through 235 Processing sheet with id=AA3, first strand: chain 'B' and resid 233 through 235 removed outlier: 5.686A pdb=" N ALA B 323 " --> pdb=" O VAL B 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 233 through 235 659 hydrogen bonds defined for protein. 1959 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: 3.46 Time building geometry restraints manager: 5.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2922 1.34 - 1.46: 2236 1.46 - 1.58: 4620 1.58 - 1.70: 0 1.70 - 1.81: 76 Bond restraints: 9854 Sorted by residual: bond pdb=" CB THR A 173 " pdb=" CG2 THR A 173 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.03e+00 bond pdb=" CB THR B 173 " pdb=" CG2 THR B 173 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 3.99e+00 bond pdb=" CZ ARG B 29 " pdb=" NH2 ARG B 29 " ideal model delta sigma weight residual 1.330 1.307 0.023 1.30e-02 5.92e+03 3.17e+00 bond pdb=" CZ ARG A 29 " pdb=" NH2 ARG A 29 " ideal model delta sigma weight residual 1.330 1.307 0.023 1.30e-02 5.92e+03 3.15e+00 bond pdb=" N ILE B 714 " pdb=" CA ILE B 714 " ideal model delta sigma weight residual 1.459 1.438 0.021 1.25e-02 6.40e+03 2.89e+00 ... (remaining 9849 not shown) Histogram of bond angle deviations from ideal: 98.30 - 105.45: 246 105.45 - 112.60: 5163 112.60 - 119.76: 3196 119.76 - 126.91: 4686 126.91 - 134.06: 147 Bond angle restraints: 13438 Sorted by residual: angle pdb=" N PRO B 275 " pdb=" CA PRO B 275 " pdb=" CB PRO B 275 " ideal model delta sigma weight residual 103.00 110.45 -7.45 1.10e+00 8.26e-01 4.59e+01 angle pdb=" N PRO A 275 " pdb=" CA PRO A 275 " pdb=" CB PRO A 275 " ideal model delta sigma weight residual 103.00 110.44 -7.44 1.10e+00 8.26e-01 4.58e+01 angle pdb=" C ASN B 612 " pdb=" N VAL B 613 " pdb=" CA VAL B 613 " ideal model delta sigma weight residual 123.16 117.82 5.34 1.06e+00 8.90e-01 2.54e+01 angle pdb=" C ASN A 612 " pdb=" N VAL A 613 " pdb=" CA VAL A 613 " ideal model delta sigma weight residual 123.16 117.85 5.31 1.06e+00 8.90e-01 2.51e+01 angle pdb=" N ILE B 714 " pdb=" CA ILE B 714 " pdb=" C ILE B 714 " ideal model delta sigma weight residual 109.34 101.30 8.04 2.08e+00 2.31e-01 1.49e+01 ... (remaining 13433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 5193 17.43 - 34.87: 407 34.87 - 52.30: 94 52.30 - 69.74: 28 69.74 - 87.17: 8 Dihedral angle restraints: 5730 sinusoidal: 2132 harmonic: 3598 Sorted by residual: dihedral pdb=" CA LEU A 703 " pdb=" C LEU A 703 " pdb=" N ASN A 704 " pdb=" CA ASN A 704 " ideal model delta harmonic sigma weight residual 180.00 156.95 23.05 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA LEU B 703 " pdb=" C LEU B 703 " pdb=" N ASN B 704 " pdb=" CA ASN B 704 " ideal model delta harmonic sigma weight residual 180.00 156.99 23.01 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA ASP B 316 " pdb=" C ASP B 316 " pdb=" N GLN B 317 " pdb=" CA GLN B 317 " ideal model delta harmonic sigma weight residual 180.00 -160.13 -19.87 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 5727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1176 0.049 - 0.098: 318 0.098 - 0.147: 44 0.147 - 0.195: 4 0.195 - 0.244: 6 Chirality restraints: 1548 Sorted by residual: chirality pdb=" CA PRO B 275 " pdb=" N PRO B 275 " pdb=" C PRO B 275 " pdb=" CB PRO B 275 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA PRO A 275 " pdb=" N PRO A 275 " pdb=" C PRO A 275 " pdb=" CB PRO A 275 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ILE B 714 " pdb=" N ILE B 714 " pdb=" C ILE B 714 " pdb=" CB ILE B 714 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 1545 not shown) Planarity restraints: 1666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 715 " 0.050 5.00e-02 4.00e+02 7.56e-02 9.15e+00 pdb=" N PRO A 716 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 716 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 716 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 715 " -0.050 5.00e-02 4.00e+02 7.56e-02 9.14e+00 pdb=" N PRO B 716 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO B 716 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 716 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 181 " 0.007 2.00e-02 2.50e+03 1.44e-02 4.16e+00 pdb=" CG TYR B 181 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR B 181 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR B 181 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR B 181 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 181 " -0.028 2.00e-02 2.50e+03 pdb=" CZ TYR B 181 " 0.020 2.00e-02 2.50e+03 pdb=" OH TYR B 181 " 0.004 2.00e-02 2.50e+03 ... (remaining 1663 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2523 2.79 - 3.32: 10181 3.32 - 3.84: 17986 3.84 - 4.37: 20781 4.37 - 4.90: 33304 Nonbonded interactions: 84775 Sorted by model distance: nonbonded pdb=" O ASN B 208 " pdb=" N TRP B 349 " model vdw 2.259 2.520 nonbonded pdb=" O ASN A 208 " pdb=" N TRP A 349 " model vdw 2.259 2.520 nonbonded pdb=" O ALA A 91 " pdb=" OG SER A 95 " model vdw 2.271 2.440 nonbonded pdb=" O ALA B 91 " pdb=" OG SER B 95 " model vdw 2.271 2.440 nonbonded pdb=" O ILE A 13 " pdb=" OG1 THR A 17 " model vdw 2.278 2.440 ... (remaining 84770 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' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 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: 4.250 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 33.290 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 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 : 0.005 0.066 9854 Z= 0.298 Angle : 0.755 8.207 13438 Z= 0.414 Chirality : 0.045 0.244 1548 Planarity : 0.006 0.076 1666 Dihedral : 14.349 87.173 3390 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.45 % Favored : 94.04 % Rotamer: Outliers : 4.55 % Allowed : 13.04 % Favored : 82.40 % 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: -3.54 (0.21), residues: 1192 helix: -1.88 (0.15), residues: 832 sheet: -3.40 (0.87), residues: 24 loop : -3.03 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 625 HIS 0.009 0.002 HIS B 608 PHE 0.017 0.002 PHE B 669 TYR 0.028 0.002 TYR B 181 ARG 0.004 0.001 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 398 time to evaluate : 1.256 Fit side-chains revert: symmetry clash outliers start: 44 outliers final: 13 residues processed: 418 average time/residue: 0.1974 time to fit residues: 118.2608 Evaluate side-chains 291 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 278 time to evaluate : 1.103 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0903 time to fit residues: 3.6654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9854 Z= 0.248 Angle : 0.742 8.102 13438 Z= 0.375 Chirality : 0.045 0.286 1548 Planarity : 0.006 0.066 1666 Dihedral : 5.392 20.283 1312 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 21.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 4.24 % Allowed : 20.50 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.23), residues: 1192 helix: -0.70 (0.17), residues: 858 sheet: -3.67 (0.88), residues: 24 loop : -3.23 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 625 HIS 0.005 0.001 HIS B 294 PHE 0.043 0.003 PHE A 21 TYR 0.027 0.002 TYR A 361 ARG 0.005 0.001 ARG B 683 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 335 time to evaluate : 1.030 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 21 residues processed: 358 average time/residue: 0.1882 time to fit residues: 97.3970 Evaluate side-chains 315 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 294 time to evaluate : 1.016 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.0918 time to fit residues: 4.9407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 10.0000 chunk 34 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 119 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 GLN ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 HIS B 339 GLN ** B 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9854 Z= 0.238 Angle : 0.724 9.230 13438 Z= 0.361 Chirality : 0.044 0.293 1548 Planarity : 0.005 0.058 1666 Dihedral : 5.223 20.919 1312 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 21.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 4.35 % Allowed : 22.26 % Favored : 73.40 % 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 (0.24), residues: 1192 helix: -0.21 (0.17), residues: 850 sheet: -3.76 (0.88), residues: 24 loop : -2.89 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 625 HIS 0.003 0.001 HIS B 294 PHE 0.016 0.002 PHE B 452 TYR 0.020 0.002 TYR A 102 ARG 0.006 0.001 ARG B 344 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 332 time to evaluate : 1.170 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 18 residues processed: 353 average time/residue: 0.1743 time to fit residues: 91.9268 Evaluate side-chains 310 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 292 time to evaluate : 1.065 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1207 time to fit residues: 5.0504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 117 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 ASN ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9854 Z= 0.238 Angle : 0.729 9.527 13438 Z= 0.361 Chirality : 0.044 0.230 1548 Planarity : 0.005 0.057 1666 Dihedral : 5.144 20.479 1312 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.11 % Allowed : 25.16 % Favored : 71.74 % 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: -1.26 (0.24), residues: 1192 helix: 0.02 (0.17), residues: 850 sheet: -3.99 (0.89), residues: 24 loop : -2.80 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 625 HIS 0.004 0.001 HIS B 608 PHE 0.048 0.002 PHE A 21 TYR 0.028 0.002 TYR A 361 ARG 0.004 0.000 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 314 time to evaluate : 1.012 Fit side-chains outliers start: 30 outliers final: 18 residues processed: 328 average time/residue: 0.1631 time to fit residues: 81.1349 Evaluate side-chains 300 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 282 time to evaluate : 1.188 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1102 time to fit residues: 5.2489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 GLN A 715 HIS ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9854 Z= 0.266 Angle : 0.742 12.132 13438 Z= 0.368 Chirality : 0.045 0.295 1548 Planarity : 0.005 0.053 1666 Dihedral : 5.089 20.637 1312 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.28 % Allowed : 28.47 % Favored : 69.25 % 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: -0.95 (0.24), residues: 1192 helix: 0.22 (0.18), residues: 842 sheet: -3.69 (0.91), residues: 24 loop : -2.53 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 75 HIS 0.005 0.001 HIS B 162 PHE 0.039 0.002 PHE B 21 TYR 0.021 0.002 TYR B 102 ARG 0.002 0.000 ARG B 683 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 298 time to evaluate : 1.166 Fit side-chains outliers start: 22 outliers final: 18 residues processed: 301 average time/residue: 0.1609 time to fit residues: 73.9623 Evaluate side-chains 293 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 275 time to evaluate : 1.142 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.0947 time to fit residues: 4.5429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 69 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 113 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9854 Z= 0.240 Angle : 0.747 16.248 13438 Z= 0.366 Chirality : 0.045 0.279 1548 Planarity : 0.005 0.053 1666 Dihedral : 4.996 19.915 1312 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 21.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 1.86 % Allowed : 29.81 % Favored : 68.32 % 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: -0.77 (0.25), residues: 1192 helix: 0.36 (0.18), residues: 842 sheet: -3.55 (0.92), residues: 24 loop : -2.47 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 75 HIS 0.006 0.001 HIS A 162 PHE 0.055 0.002 PHE A 21 TYR 0.024 0.002 TYR B 102 ARG 0.003 0.000 ARG B 683 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 297 time to evaluate : 1.236 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 304 average time/residue: 0.1753 time to fit residues: 80.0757 Evaluate side-chains 293 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 282 time to evaluate : 1.135 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0958 time to fit residues: 3.6015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 86 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 65 optimal weight: 0.0870 chunk 117 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 71 optimal weight: 0.0570 chunk 54 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN A 575 GLN ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9854 Z= 0.228 Angle : 0.766 15.762 13438 Z= 0.374 Chirality : 0.044 0.259 1548 Planarity : 0.005 0.056 1666 Dihedral : 4.949 19.413 1312 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 22.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.28 % Allowed : 30.95 % Favored : 66.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.25), residues: 1192 helix: 0.45 (0.18), residues: 832 sheet: -3.60 (0.89), residues: 24 loop : -2.33 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 75 HIS 0.006 0.001 HIS A 162 PHE 0.064 0.002 PHE A 21 TYR 0.029 0.002 TYR A 361 ARG 0.004 0.000 ARG B 683 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 306 time to evaluate : 1.136 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 15 residues processed: 311 average time/residue: 0.1774 time to fit residues: 81.4536 Evaluate side-chains 296 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 281 time to evaluate : 1.105 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0992 time to fit residues: 4.1586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 74 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 0.0030 chunk 92 optimal weight: 0.6980 chunk 106 optimal weight: 0.0980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9854 Z= 0.240 Angle : 0.794 17.117 13438 Z= 0.387 Chirality : 0.045 0.226 1548 Planarity : 0.005 0.056 1666 Dihedral : 4.941 19.028 1312 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 22.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 1.14 % Allowed : 32.92 % Favored : 65.94 % 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: -0.73 (0.25), residues: 1192 helix: 0.41 (0.18), residues: 852 sheet: -3.54 (0.90), residues: 24 loop : -2.63 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 172 HIS 0.007 0.001 HIS A 608 PHE 0.072 0.002 PHE A 21 TYR 0.030 0.002 TYR A 577 ARG 0.005 0.000 ARG B 631 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 287 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 289 average time/residue: 0.1851 time to fit residues: 78.7786 Evaluate side-chains 271 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 265 time to evaluate : 1.125 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0952 time to fit residues: 2.5207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 99 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 71 optimal weight: 0.0020 chunk 115 optimal weight: 0.9980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.5082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 9854 Z= 0.246 Angle : 0.803 16.752 13438 Z= 0.391 Chirality : 0.045 0.222 1548 Planarity : 0.005 0.056 1666 Dihedral : 4.924 20.803 1312 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 1.35 % Allowed : 33.85 % Favored : 64.80 % 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: -0.49 (0.25), residues: 1192 helix: 0.58 (0.18), residues: 840 sheet: -3.47 (0.92), residues: 24 loop : -2.40 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP A 172 HIS 0.005 0.001 HIS A 608 PHE 0.069 0.002 PHE A 21 TYR 0.031 0.002 TYR A 361 ARG 0.005 0.000 ARG B 631 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 290 time to evaluate : 1.088 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 293 average time/residue: 0.1745 time to fit residues: 76.7000 Evaluate side-chains 279 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 272 time to evaluate : 1.140 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1059 time to fit residues: 2.8369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 chunk 121 optimal weight: 0.0870 chunk 111 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 10 optimal weight: 0.0870 chunk 74 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 overall best weight: 0.5936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9854 Z= 0.247 Angle : 0.823 17.540 13438 Z= 0.401 Chirality : 0.045 0.229 1548 Planarity : 0.005 0.055 1666 Dihedral : 4.943 21.782 1312 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 1.04 % Allowed : 35.20 % Favored : 63.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.25), residues: 1192 helix: 0.55 (0.18), residues: 844 sheet: -3.31 (0.96), residues: 24 loop : -2.48 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP B 172 HIS 0.008 0.001 HIS B 162 PHE 0.071 0.002 PHE A 21 TYR 0.029 0.002 TYR A 361 ARG 0.008 0.001 ARG B 631 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 286 time to evaluate : 1.074 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 290 average time/residue: 0.1731 time to fit residues: 75.5390 Evaluate side-chains 269 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 266 time to evaluate : 1.109 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0922 time to fit residues: 2.0071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.135222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.118761 restraints weight = 18284.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.122146 restraints weight = 8249.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.124314 restraints weight = 4774.386| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 9854 Z= 0.265 Angle : 0.841 17.280 13438 Z= 0.411 Chirality : 0.046 0.235 1548 Planarity : 0.005 0.053 1666 Dihedral : 4.939 20.395 1312 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 21.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 1.14 % Allowed : 35.40 % Favored : 63.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.25), residues: 1192 helix: 0.52 (0.18), residues: 842 sheet: -3.01 (1.04), residues: 24 loop : -2.49 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP B 172 HIS 0.006 0.001 HIS A 608 PHE 0.070 0.002 PHE A 21 TYR 0.029 0.002 TYR A 361 ARG 0.006 0.001 ARG B 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2346.10 seconds wall clock time: 43 minutes 16.54 seconds (2596.54 seconds total)