Starting phenix.real_space_refine on Thu May 9 01:08:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xaj_38200/05_2024/8xaj_38200_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xaj_38200/05_2024/8xaj_38200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xaj_38200/05_2024/8xaj_38200.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xaj_38200/05_2024/8xaj_38200.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xaj_38200/05_2024/8xaj_38200_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xaj_38200/05_2024/8xaj_38200_updated.pdb" } resolution = 3.29 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= 0.017 sd= 0.074 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 P 7 5.49 5 S 52 5.16 5 C 7776 2.51 5 N 1847 2.21 5 O 1986 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 29": "NH1" <-> "NH2" Residue "A PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 137": "NH1" <-> "NH2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A GLU 219": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A GLU 677": "OE1" <-> "OE2" Residue "B ARG 29": "NH1" <-> "NH2" Residue "B PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B GLU 219": "OE1" <-> "OE2" Residue "B GLU 308": "OE1" <-> "OE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B GLU 531": "OE1" <-> "OE2" Residue "B ARG 606": "NH1" <-> "NH2" Residue "B GLU 677": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 11668 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 705, 5645 Classifications: {'peptide': 705} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 36, 'TRANS': 668} Chain breaks: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 5645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 705, 5645 Classifications: {'peptide': 705} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 36, 'TRANS': 668} Chain breaks: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "A" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 378 Unusual residues: {'PCW': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N PCW A 801 " occ=0.00 ... (52 atoms not shown) pdb=" P PCW A 801 " occ=0.00 residue: pdb=" N PCW A 802 " occ=0.00 ... (52 atoms not shown) pdb=" P PCW A 802 " occ=0.00 residue: pdb=" N PCW A 803 " occ=0.00 ... (52 atoms not shown) pdb=" P PCW A 803 " occ=0.00 residue: pdb=" N PCW A 804 " occ=0.00 ... (52 atoms not shown) pdb=" P PCW A 804 " occ=0.00 residue: pdb=" N PCW A 805 " occ=0.00 ... (52 atoms not shown) pdb=" P PCW A 805 " occ=0.00 residue: pdb=" N PCW A 806 " occ=0.00 ... (52 atoms not shown) pdb=" P PCW A 806 " occ=0.00 residue: pdb=" N PCW A 807 " occ=0.00 ... (52 atoms not shown) pdb=" P PCW A 807 " occ=0.00 Time building chain proxies: 8.23, per 1000 atoms: 0.71 Number of scatterers: 11668 At special positions: 0 Unit cell: (98.115, 148.755, 99.17, 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 52 16.00 P 7 15.00 O 1986 8.00 N 1847 7.00 C 7776 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=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.70 Conformation dependent library (CDL) restraints added in 2.3 seconds 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2712 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 2 sheets defined 61.6% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.56 Creating SS restraints... Processing helix chain 'A' and resid 4 through 27 removed outlier: 3.678A pdb=" N ALA A 26 " --> pdb=" O PHE A 22 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 73 through 76 No H-bonds generated for 'chain 'A' and resid 73 through 76' Processing helix chain 'A' and resid 84 through 91 Processing helix chain 'A' and resid 93 through 124 removed outlier: 4.592A pdb=" N TYR A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) Proline residue: A 111 - end of helix Proline residue: A 122 - end of helix Processing helix chain 'A' and resid 134 through 136 No H-bonds generated for 'chain 'A' and resid 134 through 136' Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 157 through 193 removed outlier: 4.527A pdb=" N GLU A 180 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA A 193 " --> pdb=" O GLN A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 202 Processing helix chain 'A' and resid 217 through 227 Processing helix chain 'A' and resid 244 through 268 Processing helix chain 'A' and resid 292 through 312 removed outlier: 3.937A pdb=" N GLU A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 338 Processing helix chain 'A' and resid 368 through 387 Processing helix chain 'A' and resid 391 through 399 Processing helix chain 'A' and resid 409 through 411 No H-bonds generated for 'chain 'A' and resid 409 through 411' Processing helix chain 'A' and resid 423 through 451 Proline residue: A 430 - end of helix removed outlier: 3.664A pdb=" N LEU A 434 " --> pdb=" O PRO A 430 " (cutoff:3.500A) Proline residue: A 442 - end of helix Processing helix chain 'A' and resid 457 through 481 Processing helix chain 'A' and resid 486 through 495 Processing helix chain 'A' and resid 501 through 532 Proline residue: A 510 - end of helix removed outlier: 4.593A pdb=" N THR A 514 " --> pdb=" O PRO A 510 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE A 515 " --> pdb=" O MET A 511 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 532 " --> pdb=" O VAL A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 547 removed outlier: 3.685A pdb=" N LEU A 543 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA A 546 " --> pdb=" O HIS A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 582 Processing helix chain 'A' and resid 588 through 611 Proline residue: A 592 - end of helix removed outlier: 5.112A pdb=" N TYR A 605 " --> pdb=" O TYR A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 648 Processing helix chain 'A' and resid 655 through 675 Proline residue: A 662 - end of helix Processing helix chain 'A' and resid 677 through 680 Processing helix chain 'A' and resid 685 through 698 Processing helix chain 'A' and resid 704 through 708 Processing helix chain 'B' and resid 4 through 27 removed outlier: 3.679A pdb=" N ALA B 26 " --> pdb=" O PHE B 22 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL B 27 " --> pdb=" O ILE B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'B' and resid 73 through 76 No H-bonds generated for 'chain 'B' and resid 73 through 76' Processing helix chain 'B' and resid 84 through 91 Processing helix chain 'B' and resid 93 through 124 removed outlier: 4.592A pdb=" N TYR B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) Proline residue: B 111 - end of helix Proline residue: B 122 - end of helix Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 138 through 140 No H-bonds generated for 'chain 'B' and resid 138 through 140' Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 157 through 193 removed outlier: 4.527A pdb=" N GLU B 180 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA B 193 " --> pdb=" O GLN B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 202 Processing helix chain 'B' and resid 217 through 227 Processing helix chain 'B' and resid 244 through 268 Processing helix chain 'B' and resid 292 through 312 removed outlier: 3.936A pdb=" N GLU B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU B 311 " --> pdb=" O LYS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 338 Processing helix chain 'B' and resid 368 through 387 Processing helix chain 'B' and resid 391 through 399 Processing helix chain 'B' and resid 409 through 411 No H-bonds generated for 'chain 'B' and resid 409 through 411' Processing helix chain 'B' and resid 423 through 451 Proline residue: B 430 - end of helix removed outlier: 3.664A pdb=" N LEU B 434 " --> pdb=" O PRO B 430 " (cutoff:3.500A) Proline residue: B 442 - end of helix Processing helix chain 'B' and resid 457 through 481 Processing helix chain 'B' and resid 486 through 495 Processing helix chain 'B' and resid 501 through 532 Proline residue: B 510 - end of helix removed outlier: 4.593A pdb=" N THR B 514 " --> pdb=" O PRO B 510 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE B 515 " --> pdb=" O MET B 511 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE B 532 " --> pdb=" O VAL B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 547 removed outlier: 3.686A pdb=" N LEU B 543 " --> pdb=" O ILE B 539 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA B 546 " --> pdb=" O HIS B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 582 Processing helix chain 'B' and resid 588 through 611 Proline residue: B 592 - end of helix removed outlier: 5.113A pdb=" N TYR B 605 " --> pdb=" O TYR B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 648 Processing helix chain 'B' and resid 655 through 675 Proline residue: B 662 - end of helix Processing helix chain 'B' and resid 677 through 680 Processing helix chain 'B' and resid 685 through 698 Processing helix chain 'B' and resid 704 through 708 Processing sheet with id= A, first strand: chain 'A' and resid 349 through 352 Processing sheet with id= B, first strand: chain 'B' and resid 349 through 352 608 hydrogen bonds defined for protein. 1506 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: 4.36 Time building geometry restraints manager: 6.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1762 1.31 - 1.44: 3314 1.44 - 1.56: 6753 1.56 - 1.69: 52 1.69 - 1.81: 96 Bond restraints: 11977 Sorted by residual: bond pdb=" C14 PCW A 804 " pdb=" C15 PCW A 804 " ideal model delta sigma weight residual 1.523 1.630 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C11 PCW A 807 " pdb=" O3 PCW A 807 " ideal model delta sigma weight residual 1.326 1.429 -0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" C11 PCW A 804 " pdb=" O3 PCW A 804 " ideal model delta sigma weight residual 1.326 1.428 -0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C11 PCW A 806 " pdb=" O3 PCW A 806 " ideal model delta sigma weight residual 1.326 1.428 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C11 PCW A 801 " pdb=" O3 PCW A 801 " ideal model delta sigma weight residual 1.326 1.427 -0.101 2.00e-02 2.50e+03 2.55e+01 ... (remaining 11972 not shown) Histogram of bond angle deviations from ideal: 95.72 - 103.39: 161 103.39 - 111.05: 4450 111.05 - 118.72: 5033 118.72 - 126.38: 6367 126.38 - 134.04: 210 Bond angle restraints: 16221 Sorted by residual: angle pdb=" O3P PCW A 802 " pdb=" P PCW A 802 " pdb=" O4P PCW A 802 " ideal model delta sigma weight residual 96.85 111.25 -14.40 3.00e+00 1.11e-01 2.30e+01 angle pdb=" C5 PCW A 803 " pdb=" N PCW A 803 " pdb=" C7 PCW A 803 " ideal model delta sigma weight residual 107.31 120.91 -13.60 3.00e+00 1.11e-01 2.05e+01 angle pdb=" C5 PCW A 802 " pdb=" N PCW A 802 " pdb=" C7 PCW A 802 " ideal model delta sigma weight residual 107.31 120.83 -13.52 3.00e+00 1.11e-01 2.03e+01 angle pdb=" C ARG B 675 " pdb=" CA ARG B 675 " pdb=" CB ARG B 675 " ideal model delta sigma weight residual 111.03 102.78 8.25 1.87e+00 2.86e-01 1.95e+01 angle pdb=" O3P PCW A 801 " pdb=" P PCW A 801 " pdb=" O4P PCW A 801 " ideal model delta sigma weight residual 96.85 109.97 -13.12 3.00e+00 1.11e-01 1.91e+01 ... (remaining 16216 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.56: 6939 34.56 - 69.12: 196 69.12 - 103.68: 18 103.68 - 138.24: 4 138.24 - 172.80: 2 Dihedral angle restraints: 7159 sinusoidal: 2985 harmonic: 4174 Sorted by residual: dihedral pdb=" CA ARG B 682 " pdb=" C ARG B 682 " pdb=" N TYR B 683 " pdb=" CA TYR B 683 " ideal model delta harmonic sigma weight residual -180.00 -152.82 -27.18 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA ARG A 682 " pdb=" C ARG A 682 " pdb=" N TYR A 683 " pdb=" CA TYR A 683 " ideal model delta harmonic sigma weight residual 180.00 -152.83 -27.17 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA VAL B 612 " pdb=" C VAL B 612 " pdb=" N TYR B 613 " pdb=" CA TYR B 613 " ideal model delta harmonic sigma weight residual 180.00 154.17 25.83 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 7156 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1449 0.058 - 0.116: 290 0.116 - 0.174: 40 0.174 - 0.232: 10 0.232 - 0.290: 4 Chirality restraints: 1793 Sorted by residual: chirality pdb=" C2 PCW A 807 " pdb=" C1 PCW A 807 " pdb=" C3 PCW A 807 " pdb=" O2 PCW A 807 " both_signs ideal model delta sigma weight residual False -2.32 -2.61 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C2 PCW A 805 " pdb=" C1 PCW A 805 " pdb=" C3 PCW A 805 " pdb=" O2 PCW A 805 " both_signs ideal model delta sigma weight residual False -2.32 -2.58 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C2 PCW A 804 " pdb=" C1 PCW A 804 " pdb=" C3 PCW A 804 " pdb=" O2 PCW A 804 " both_signs ideal model delta sigma weight residual False -2.32 -2.56 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 1790 not shown) Planarity restraints: 2002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C38 PCW A 804 " 0.022 2.00e-02 2.50e+03 3.97e-02 1.58e+01 pdb=" C39 PCW A 804 " -0.050 2.00e-02 2.50e+03 pdb=" C40 PCW A 804 " 0.052 2.00e-02 2.50e+03 pdb=" C41 PCW A 804 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 84 " 0.059 5.00e-02 4.00e+02 8.93e-02 1.28e+01 pdb=" N PRO A 85 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 84 " -0.059 5.00e-02 4.00e+02 8.93e-02 1.27e+01 pdb=" N PRO B 85 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO B 85 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 85 " -0.050 5.00e-02 4.00e+02 ... (remaining 1999 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 8 2.22 - 2.89: 4717 2.89 - 3.56: 17656 3.56 - 4.23: 25944 4.23 - 4.90: 44668 Nonbonded interactions: 92993 Sorted by model distance: nonbonded pdb=" NH1 ARG A 188 " pdb=" O ALA A 620 " model vdw 1.547 2.520 nonbonded pdb=" NH1 ARG B 188 " pdb=" O ALA B 620 " model vdw 1.550 2.520 nonbonded pdb=" NH1 ARG A 188 " pdb=" C ALA A 620 " model vdw 2.088 3.350 nonbonded pdb=" NH1 ARG B 188 " pdb=" C ALA B 620 " model vdw 2.092 3.350 nonbonded pdb=" ND2 ASN A 257 " pdb=" OD2 ASP A 554 " model vdw 2.194 2.520 ... (remaining 92988 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 3 through 718) 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=0.00 max=1.00 mean=0.97 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: 1.690 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: 0.000 Extract box with map and model: 3.860 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 39.850 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.070 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: 49.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 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 : 0.009 0.107 11977 Z= 0.580 Angle : 1.091 14.398 16221 Z= 0.519 Chirality : 0.050 0.290 1793 Planarity : 0.007 0.089 2002 Dihedral : 16.782 172.801 4447 Min Nonbonded Distance : 1.547 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.22), residues: 1402 helix: 0.13 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -2.81 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 624 HIS 0.004 0.001 HIS A 90 PHE 0.017 0.002 PHE B 598 TYR 0.030 0.002 TYR B 181 ARG 0.014 0.001 ARG B 630 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.237 Fit side-chains revert: symmetry clash REVERT: A 303 LYS cc_start: 0.9221 (tptm) cc_final: 0.8987 (tptp) REVERT: A 307 LYS cc_start: 0.8231 (tptp) cc_final: 0.7897 (tptp) REVERT: A 650 HIS cc_start: 0.7976 (m170) cc_final: 0.7753 (m170) REVERT: B 165 MET cc_start: 0.8072 (mmp) cc_final: 0.7587 (mmp) REVERT: B 167 TYR cc_start: 0.8730 (m-80) cc_final: 0.8447 (m-80) REVERT: B 300 LYS cc_start: 0.8883 (mtmm) cc_final: 0.8374 (mtmt) REVERT: B 303 LYS cc_start: 0.9190 (tptm) cc_final: 0.8952 (mmmm) REVERT: B 307 LYS cc_start: 0.8374 (tptp) cc_final: 0.8018 (tptp) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.2621 time to fit residues: 72.8571 Evaluate side-chains 155 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 109 optimal weight: 40.0000 chunk 42 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 ASN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11977 Z= 0.211 Angle : 0.699 7.927 16221 Z= 0.358 Chirality : 0.043 0.160 1793 Planarity : 0.006 0.066 2002 Dihedral : 14.632 150.642 1831 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 1.34 % Allowed : 7.39 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.23), residues: 1402 helix: 0.50 (0.19), residues: 828 sheet: -1.91 (1.05), residues: 24 loop : -2.80 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 624 HIS 0.003 0.001 HIS B 232 PHE 0.032 0.001 PHE A 72 TYR 0.020 0.002 TYR B 181 ARG 0.016 0.001 ARG B 630 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 176 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 LYS cc_start: 0.9166 (tptm) cc_final: 0.8930 (tptp) REVERT: A 307 LYS cc_start: 0.8309 (tptp) cc_final: 0.8000 (tptp) REVERT: A 559 MET cc_start: 0.3333 (ptt) cc_final: 0.2932 (ptt) REVERT: A 589 MET cc_start: 0.8061 (mmm) cc_final: 0.7850 (mmm) REVERT: A 613 TYR cc_start: 0.6774 (m-80) cc_final: 0.6340 (m-80) REVERT: B 165 MET cc_start: 0.7998 (mmp) cc_final: 0.7569 (mmt) REVERT: B 167 TYR cc_start: 0.8681 (m-80) cc_final: 0.8385 (m-80) REVERT: B 303 LYS cc_start: 0.9155 (tptm) cc_final: 0.8927 (tptp) REVERT: B 307 LYS cc_start: 0.8422 (tptp) cc_final: 0.8044 (tptp) REVERT: B 521 MET cc_start: 0.6910 (OUTLIER) cc_final: 0.6575 (mpp) REVERT: B 613 TYR cc_start: 0.6820 (m-80) cc_final: 0.6383 (m-80) outliers start: 16 outliers final: 5 residues processed: 181 average time/residue: 0.2333 time to fit residues: 61.9298 Evaluate side-chains 167 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 161 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 521 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 10.0000 chunk 39 optimal weight: 50.0000 chunk 105 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 574 GLN ** B 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11977 Z= 0.270 Angle : 0.691 8.418 16221 Z= 0.357 Chirality : 0.044 0.162 1793 Planarity : 0.006 0.058 2002 Dihedral : 14.202 153.357 1831 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % Rotamer: Outliers : 2.52 % Allowed : 10.76 % Favored : 86.72 % 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: -1.05 (0.23), residues: 1402 helix: 0.61 (0.19), residues: 822 sheet: -1.11 (1.13), residues: 22 loop : -2.78 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 624 HIS 0.003 0.001 HIS A 628 PHE 0.032 0.002 PHE B 72 TYR 0.023 0.002 TYR B 181 ARG 0.015 0.001 ARG B 630 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 171 time to evaluate : 1.296 Fit side-chains revert: symmetry clash REVERT: A 70 MET cc_start: 0.6599 (mmt) cc_final: 0.6383 (mmp) REVERT: A 297 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.6216 (mp0) REVERT: A 303 LYS cc_start: 0.9155 (tptm) cc_final: 0.8905 (tptp) REVERT: A 307 LYS cc_start: 0.8355 (tptp) cc_final: 0.8036 (tptp) REVERT: A 521 MET cc_start: 0.6704 (OUTLIER) cc_final: 0.5884 (mpp) REVERT: A 613 TYR cc_start: 0.7133 (m-80) cc_final: 0.6630 (m-80) REVERT: B 124 ASN cc_start: 0.8206 (OUTLIER) cc_final: 0.7970 (t0) REVERT: B 165 MET cc_start: 0.8016 (mmp) cc_final: 0.7570 (mmt) REVERT: B 167 TYR cc_start: 0.8674 (m-80) cc_final: 0.8406 (m-80) REVERT: B 297 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6663 (mp0) REVERT: B 303 LYS cc_start: 0.9163 (tptm) cc_final: 0.8932 (tptp) REVERT: B 307 LYS cc_start: 0.8479 (tptp) cc_final: 0.8146 (tptp) REVERT: B 613 TYR cc_start: 0.7090 (m-80) cc_final: 0.6606 (m-80) outliers start: 30 outliers final: 16 residues processed: 185 average time/residue: 0.2202 time to fit residues: 60.1668 Evaluate side-chains 180 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 160 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 653 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 127 optimal weight: 4.9990 chunk 135 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 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 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11977 Z= 0.199 Angle : 0.658 7.745 16221 Z= 0.341 Chirality : 0.042 0.159 1793 Planarity : 0.006 0.058 2002 Dihedral : 13.796 162.997 1831 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 1.93 % Allowed : 14.54 % Favored : 83.53 % 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: -0.89 (0.24), residues: 1402 helix: 0.71 (0.19), residues: 820 sheet: -1.15 (1.11), residues: 22 loop : -2.65 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 624 HIS 0.002 0.001 HIS B 232 PHE 0.030 0.001 PHE A 389 TYR 0.020 0.001 TYR B 181 ARG 0.016 0.000 ARG B 630 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 168 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.6561 (mmt) cc_final: 0.6339 (mmp) REVERT: A 297 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.6264 (mp0) REVERT: A 303 LYS cc_start: 0.9151 (tptm) cc_final: 0.8894 (tptp) REVERT: A 307 LYS cc_start: 0.8340 (tptp) cc_final: 0.8102 (tptp) REVERT: A 521 MET cc_start: 0.6460 (OUTLIER) cc_final: 0.5630 (mpp) REVERT: A 613 TYR cc_start: 0.7032 (m-80) cc_final: 0.6510 (m-80) REVERT: B 167 TYR cc_start: 0.8662 (m-80) cc_final: 0.8440 (m-80) REVERT: B 297 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6503 (mp0) REVERT: B 303 LYS cc_start: 0.9160 (tptm) cc_final: 0.8895 (tptp) REVERT: B 307 LYS cc_start: 0.8470 (tptp) cc_final: 0.8147 (tptp) REVERT: B 613 TYR cc_start: 0.7109 (m-80) cc_final: 0.6640 (m-80) outliers start: 23 outliers final: 11 residues processed: 181 average time/residue: 0.2202 time to fit residues: 59.0164 Evaluate side-chains 166 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 152 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 594 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11977 Z= 0.286 Angle : 0.685 8.321 16221 Z= 0.355 Chirality : 0.044 0.164 1793 Planarity : 0.006 0.063 2002 Dihedral : 13.528 172.535 1831 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.99 % Favored : 90.01 % Rotamer: Outliers : 3.19 % Allowed : 15.46 % Favored : 81.34 % 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: -0.97 (0.23), residues: 1402 helix: 0.63 (0.19), residues: 822 sheet: -1.43 (1.21), residues: 20 loop : -2.64 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 117 HIS 0.004 0.001 HIS A 628 PHE 0.033 0.002 PHE B 72 TYR 0.027 0.002 TYR A 181 ARG 0.011 0.001 ARG A 630 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 157 time to evaluate : 1.186 Fit side-chains revert: symmetry clash REVERT: A 70 MET cc_start: 0.6599 (mmt) cc_final: 0.6381 (mmp) REVERT: A 297 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.6267 (mp0) REVERT: A 307 LYS cc_start: 0.8402 (tptp) cc_final: 0.7967 (tptp) REVERT: A 521 MET cc_start: 0.6578 (OUTLIER) cc_final: 0.5664 (mpp) REVERT: A 613 TYR cc_start: 0.7201 (m-80) cc_final: 0.6625 (m-80) REVERT: B 125 TRP cc_start: 0.7607 (t-100) cc_final: 0.7387 (t-100) REVERT: B 167 TYR cc_start: 0.8711 (m-80) cc_final: 0.8483 (m-80) REVERT: B 297 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6540 (mp0) REVERT: B 307 LYS cc_start: 0.8500 (tptp) cc_final: 0.8177 (tptp) REVERT: B 573 ILE cc_start: 0.7486 (pt) cc_final: 0.7250 (tp) REVERT: B 613 TYR cc_start: 0.7095 (m-80) cc_final: 0.6570 (m-80) outliers start: 38 outliers final: 22 residues processed: 178 average time/residue: 0.2238 time to fit residues: 59.0207 Evaluate side-chains 181 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 156 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 653 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 4.9990 chunk 26 optimal weight: 30.0000 chunk 79 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 GLN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11977 Z= 0.196 Angle : 0.656 7.813 16221 Z= 0.339 Chirality : 0.042 0.158 1793 Planarity : 0.006 0.056 2002 Dihedral : 13.272 179.756 1831 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 2.77 % Allowed : 18.07 % Favored : 79.16 % 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: -0.80 (0.24), residues: 1402 helix: 0.74 (0.19), residues: 826 sheet: -1.42 (1.20), residues: 20 loop : -2.55 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 624 HIS 0.002 0.001 HIS B 232 PHE 0.030 0.001 PHE B 72 TYR 0.023 0.001 TYR B 181 ARG 0.011 0.000 ARG B 630 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 169 time to evaluate : 1.272 Fit side-chains revert: symmetry clash REVERT: A 70 MET cc_start: 0.6559 (mmt) cc_final: 0.6344 (mmp) REVERT: A 297 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.6273 (mp0) REVERT: A 303 LYS cc_start: 0.9019 (tptp) cc_final: 0.8745 (tptp) REVERT: A 307 LYS cc_start: 0.8444 (tptp) cc_final: 0.7844 (tptp) REVERT: A 521 MET cc_start: 0.6411 (OUTLIER) cc_final: 0.5561 (mpp) REVERT: A 613 TYR cc_start: 0.7127 (m-80) cc_final: 0.6678 (m-80) REVERT: B 297 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.5638 (mp0) REVERT: B 300 LYS cc_start: 0.8928 (mtmm) cc_final: 0.8478 (mtmt) REVERT: B 303 LYS cc_start: 0.9020 (tptp) cc_final: 0.8769 (tptp) REVERT: B 304 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.7064 (pm20) REVERT: B 307 LYS cc_start: 0.8469 (tptp) cc_final: 0.8227 (tptp) REVERT: B 613 TYR cc_start: 0.7214 (m-80) cc_final: 0.6616 (m-80) outliers start: 33 outliers final: 19 residues processed: 188 average time/residue: 0.2339 time to fit residues: 64.5688 Evaluate side-chains 177 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 154 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 594 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 76 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 75 optimal weight: 0.0270 chunk 134 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 82 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- 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 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11977 Z= 0.185 Angle : 0.657 8.121 16221 Z= 0.338 Chirality : 0.042 0.157 1793 Planarity : 0.006 0.056 2002 Dihedral : 12.948 174.265 1831 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 2.35 % Allowed : 19.16 % Favored : 78.49 % 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: -0.71 (0.24), residues: 1402 helix: 0.80 (0.19), residues: 824 sheet: -1.33 (1.22), residues: 20 loop : -2.47 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 624 HIS 0.002 0.001 HIS A 650 PHE 0.032 0.001 PHE B 72 TYR 0.020 0.001 TYR B 181 ARG 0.012 0.000 ARG B 630 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 173 time to evaluate : 1.346 Fit side-chains revert: symmetry clash REVERT: A 70 MET cc_start: 0.6579 (mmt) cc_final: 0.6370 (mmp) REVERT: A 297 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.6274 (mp0) REVERT: A 307 LYS cc_start: 0.8427 (tptp) cc_final: 0.8090 (tptp) REVERT: A 521 MET cc_start: 0.6192 (OUTLIER) cc_final: 0.5273 (mpp) REVERT: A 589 MET cc_start: 0.8133 (mmm) cc_final: 0.7892 (mmm) REVERT: A 613 TYR cc_start: 0.7044 (m-80) cc_final: 0.6450 (m-80) REVERT: B 297 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6524 (mp0) REVERT: B 307 LYS cc_start: 0.8471 (tptp) cc_final: 0.8248 (tptp) REVERT: B 613 TYR cc_start: 0.7199 (m-80) cc_final: 0.6598 (m-80) outliers start: 28 outliers final: 19 residues processed: 188 average time/residue: 0.2224 time to fit residues: 62.0712 Evaluate side-chains 185 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 163 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 594 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 26 optimal weight: 50.0000 chunk 85 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11977 Z= 0.207 Angle : 0.661 8.723 16221 Z= 0.341 Chirality : 0.043 0.158 1793 Planarity : 0.006 0.055 2002 Dihedral : 12.710 170.766 1831 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.99 % Favored : 90.01 % Rotamer: Outliers : 2.61 % Allowed : 19.16 % Favored : 78.24 % 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 (0.24), residues: 1402 helix: 0.70 (0.19), residues: 836 sheet: -1.36 (1.23), residues: 20 loop : -2.49 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 624 HIS 0.002 0.001 HIS B 232 PHE 0.031 0.001 PHE B 72 TYR 0.020 0.001 TYR B 181 ARG 0.012 0.000 ARG B 630 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 172 time to evaluate : 1.528 Fit side-chains revert: symmetry clash REVERT: A 297 GLU cc_start: 0.6714 (OUTLIER) cc_final: 0.6270 (mp0) REVERT: A 307 LYS cc_start: 0.8428 (tptp) cc_final: 0.7815 (tptp) REVERT: A 521 MET cc_start: 0.6250 (OUTLIER) cc_final: 0.5301 (mpp) REVERT: A 613 TYR cc_start: 0.7035 (m-80) cc_final: 0.6423 (m-80) REVERT: B 297 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6528 (mp0) REVERT: B 303 LYS cc_start: 0.9005 (tptp) cc_final: 0.8781 (tptp) REVERT: B 304 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6960 (pm20) REVERT: B 307 LYS cc_start: 0.8482 (tptp) cc_final: 0.8244 (tptp) REVERT: B 559 MET cc_start: 0.2660 (ptt) cc_final: 0.2306 (mpp) REVERT: B 613 TYR cc_start: 0.7217 (m-80) cc_final: 0.6595 (m-80) outliers start: 31 outliers final: 23 residues processed: 191 average time/residue: 0.2255 time to fit residues: 64.2823 Evaluate side-chains 194 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 167 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 653 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 54 optimal weight: 0.0270 chunk 98 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 113 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 overall best weight: 0.7442 ------------------------------------------------------------------------------- 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 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11977 Z= 0.192 Angle : 0.664 10.763 16221 Z= 0.341 Chirality : 0.042 0.170 1793 Planarity : 0.006 0.055 2002 Dihedral : 12.425 167.140 1831 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 2.69 % Allowed : 18.99 % Favored : 78.32 % 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: -0.64 (0.24), residues: 1402 helix: 0.78 (0.19), residues: 824 sheet: -1.38 (1.22), residues: 20 loop : -2.31 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 624 HIS 0.002 0.000 HIS B 232 PHE 0.032 0.001 PHE B 72 TYR 0.016 0.001 TYR B 181 ARG 0.012 0.000 ARG B 630 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 174 time to evaluate : 1.396 Fit side-chains revert: symmetry clash REVERT: A 70 MET cc_start: 0.6817 (mmt) cc_final: 0.6616 (mmp) REVERT: A 200 ASP cc_start: 0.8218 (p0) cc_final: 0.7866 (p0) REVERT: A 297 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.6243 (mp0) REVERT: A 307 LYS cc_start: 0.8461 (tptp) cc_final: 0.8123 (tptp) REVERT: A 521 MET cc_start: 0.6291 (OUTLIER) cc_final: 0.5347 (mpp) REVERT: A 589 MET cc_start: 0.8106 (mmm) cc_final: 0.7865 (mmm) REVERT: A 613 TYR cc_start: 0.7022 (m-80) cc_final: 0.6419 (m-80) REVERT: B 297 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6516 (mp0) REVERT: B 303 LYS cc_start: 0.9009 (tptp) cc_final: 0.8756 (tptp) REVERT: B 304 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6939 (pm20) REVERT: B 307 LYS cc_start: 0.8494 (tptp) cc_final: 0.8255 (tptp) REVERT: B 559 MET cc_start: 0.2786 (ptt) cc_final: 0.2379 (mpp) REVERT: B 613 TYR cc_start: 0.7122 (m-80) cc_final: 0.6567 (m-80) outliers start: 32 outliers final: 24 residues processed: 193 average time/residue: 0.2170 time to fit residues: 62.2002 Evaluate side-chains 198 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 170 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 43 TYR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 594 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 chunk 111 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 118 optimal weight: 0.7980 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 162 HIS ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 11977 Z= 0.206 Angle : 0.678 10.951 16221 Z= 0.348 Chirality : 0.043 0.168 1793 Planarity : 0.006 0.055 2002 Dihedral : 12.212 164.071 1831 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 2.77 % Allowed : 18.91 % Favored : 78.32 % 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: -0.69 (0.24), residues: 1402 helix: 0.70 (0.19), residues: 836 sheet: -1.36 (1.22), residues: 20 loop : -2.33 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 624 HIS 0.002 0.001 HIS A 650 PHE 0.031 0.002 PHE B 72 TYR 0.011 0.001 TYR B 181 ARG 0.012 0.000 ARG B 630 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 179 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 ASP cc_start: 0.8203 (p0) cc_final: 0.7845 (p0) REVERT: A 297 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.6284 (mp0) REVERT: A 303 LYS cc_start: 0.9103 (mmmm) cc_final: 0.8645 (tptp) REVERT: A 307 LYS cc_start: 0.8458 (tptp) cc_final: 0.7810 (tptp) REVERT: A 521 MET cc_start: 0.6378 (OUTLIER) cc_final: 0.5431 (mpp) REVERT: A 589 MET cc_start: 0.8092 (mmm) cc_final: 0.7889 (mmm) REVERT: A 613 TYR cc_start: 0.7006 (m-80) cc_final: 0.6345 (m-80) REVERT: B 297 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6496 (mp0) REVERT: B 303 LYS cc_start: 0.9002 (tptp) cc_final: 0.8723 (tptp) REVERT: B 304 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6943 (pm20) REVERT: B 307 LYS cc_start: 0.8544 (tptp) cc_final: 0.8272 (tptp) REVERT: B 613 TYR cc_start: 0.7134 (m-80) cc_final: 0.6575 (m-80) outliers start: 33 outliers final: 26 residues processed: 197 average time/residue: 0.2179 time to fit residues: 64.4149 Evaluate side-chains 205 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 175 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 43 TYR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 594 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 114 optimal weight: 0.0170 chunk 14 optimal weight: 0.4980 chunk 20 optimal weight: 0.0870 chunk 97 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 overall best weight: 0.3196 ------------------------------------------------------------------------------- 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** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.183542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.144177 restraints weight = 17747.607| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.44 r_work: 0.3630 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11977 Z= 0.173 Angle : 0.660 11.267 16221 Z= 0.338 Chirality : 0.042 0.165 1793 Planarity : 0.006 0.055 2002 Dihedral : 11.946 161.208 1831 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 2.02 % Allowed : 19.92 % Favored : 78.07 % 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: -0.70 (0.24), residues: 1402 helix: 0.74 (0.19), residues: 840 sheet: -1.26 (1.25), residues: 20 loop : -2.46 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 624 HIS 0.002 0.000 HIS A 650 PHE 0.033 0.001 PHE B 72 TYR 0.012 0.001 TYR B 602 ARG 0.012 0.000 ARG A 630 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2470.08 seconds wall clock time: 46 minutes 20.92 seconds (2780.92 seconds total)