Starting phenix.real_space_refine on Sun Apr 7 15:36:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fqf_29386/04_2024/8fqf_29386.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fqf_29386/04_2024/8fqf_29386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fqf_29386/04_2024/8fqf_29386.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fqf_29386/04_2024/8fqf_29386.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fqf_29386/04_2024/8fqf_29386.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fqf_29386/04_2024/8fqf_29386.pdb" } resolution = 2.29 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= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 77 5.16 5 Cl 2 4.86 5 C 7005 2.51 5 N 1709 2.21 5 O 2102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 519": "OD1" <-> "OD2" Residue "B GLU 570": "OE1" <-> "OE2" Residue "B PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 570": "OE1" <-> "OE2" Residue "D PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 95": "OE1" <-> "OE2" Residue "E PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 31": "OD1" <-> "OD2" Residue "F ASP 31": "OD1" <-> "OD2" Residue "F TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 191": "OE1" <-> "OE2" Residue "H GLU 191": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 10895 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1177 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 149, 1165 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 149, 1165 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 1183 Chain: "B" Number of atoms: 1233 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 156, 1227 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 156, 1227 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 2 bond proxies already assigned to first conformer: 1253 Chain: "C" Number of atoms: 1183 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 149, 1165 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 149, 1165 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 1183 Conformer: "C" Number of residues, atoms: 148, 1159 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 1183 Chain: "D" Number of atoms: 1233 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 156, 1227 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 156, 1227 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 2 bond proxies already assigned to first conformer: 1253 Chain: "E" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1451 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1451 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1467 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 187} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1467 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 187} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "F" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "H" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ACYS A 589 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 589 " occ=0.50 residue: pdb=" N ASER A 615 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 615 " occ=0.50 residue: pdb=" N ACYS B 589 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 589 " occ=0.50 residue: pdb=" N ACYS C 589 " occ=0.25 ... (16 atoms not shown) pdb=" SG CCYS C 589 " occ=0.50 residue: pdb=" N ASER C 615 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER C 615 " occ=0.50 residue: pdb=" N ACYS D 589 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS D 589 " occ=0.50 Time building chain proxies: 8.48, per 1000 atoms: 0.78 Number of scatterers: 10895 At special positions: 0 Unit cell: (113.98, 113.16, 91.02, 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) Cl 2 17.00 S 77 16.00 O 2102 8.00 N 1709 7.00 C 7005 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.01 Conformation dependent library (CDL) restraints added in 3.1 seconds 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2522 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 8 sheets defined 72.8% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 546 Processing helix chain 'A' and resid 547 through 549 No H-bonds generated for 'chain 'A' and resid 547 through 549' Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 625 Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 826 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 547 through 551 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 618 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 789 through 791 No H-bonds generated for 'chain 'B' and resid 789 through 791' Processing helix chain 'B' and resid 792 through 826 Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 546 Processing helix chain 'C' and resid 547 through 549 No H-bonds generated for 'chain 'C' and resid 547 through 549' Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 625 Processing helix chain 'C' and resid 788 through 824 removed outlier: 3.777A pdb=" N VAL C 792 " --> pdb=" O SER C 788 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLY C 794 " --> pdb=" O SER C 790 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL C 795 " --> pdb=" O ASN C 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 522 through 546 Processing helix chain 'D' and resid 547 through 551 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 618 Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 789 through 791 No H-bonds generated for 'chain 'D' and resid 789 through 791' Processing helix chain 'D' and resid 792 through 826 Processing helix chain 'E' and resid 6 through 30 Processing helix chain 'E' and resid 92 through 105 Processing helix chain 'E' and resid 105 through 127 Processing helix chain 'E' and resid 132 through 161 removed outlier: 3.620A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 214 Processing helix chain 'G' and resid 6 through 30 Processing helix chain 'G' and resid 92 through 105 Processing helix chain 'G' and resid 105 through 125 Processing helix chain 'G' and resid 126 through 128 No H-bonds generated for 'chain 'G' and resid 126 through 128' Processing helix chain 'G' and resid 132 through 161 removed outlier: 3.560A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 214 Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 93 through 105 Processing helix chain 'F' and resid 105 through 129 Processing helix chain 'F' and resid 132 through 162 Processing helix chain 'F' and resid 177 through 216 Processing helix chain 'H' and resid 6 through 30 Processing helix chain 'H' and resid 93 through 105 Processing helix chain 'H' and resid 105 through 129 Processing helix chain 'H' and resid 132 through 162 Processing helix chain 'H' and resid 177 through 216 Processing sheet with id=AA1, first strand: chain 'A' and resid 551 through 552 Processing sheet with id=AA2, first strand: chain 'B' and resid 509 through 510 Processing sheet with id=AA3, first strand: chain 'C' and resid 551 through 552 Processing sheet with id=AA4, first strand: chain 'D' and resid 509 through 510 Processing sheet with id=AA5, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AA6, first strand: chain 'G' and resid 77 through 79 Processing sheet with id=AA7, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AA8, first strand: chain 'H' and resid 77 through 79 862 hydrogen bonds defined for protein. 2501 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: 3.38 Time building geometry restraints manager: 5.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3235 1.35 - 1.46: 3076 1.46 - 1.58: 4503 1.58 - 1.70: 0 1.70 - 1.82: 117 Bond restraints: 10931 Sorted by residual: bond pdb=" CB GLU H 191 " pdb=" CG GLU H 191 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.32e-01 bond pdb=" CA ASP F 5 " pdb=" CB ASP F 5 " ideal model delta sigma weight residual 1.530 1.544 -0.014 2.00e-02 2.50e+03 4.79e-01 bond pdb=" CB ASP F 5 " pdb=" CG ASP F 5 " ideal model delta sigma weight residual 1.516 1.532 -0.016 2.50e-02 1.60e+03 4.22e-01 bond pdb=" CG MET B 825 " pdb=" SD MET B 825 " ideal model delta sigma weight residual 1.803 1.819 -0.016 2.50e-02 1.60e+03 4.05e-01 bond pdb=" CG GLU H 191 " pdb=" CD GLU H 191 " ideal model delta sigma weight residual 1.516 1.532 -0.016 2.50e-02 1.60e+03 4.01e-01 ... (remaining 10926 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.22: 169 106.22 - 113.18: 5872 113.18 - 120.13: 3770 120.13 - 127.09: 4882 127.09 - 134.04: 116 Bond angle restraints: 14809 Sorted by residual: angle pdb=" CB MET B 825 " pdb=" CG MET B 825 " pdb=" SD MET B 825 " ideal model delta sigma weight residual 112.70 120.91 -8.21 3.00e+00 1.11e-01 7.49e+00 angle pdb=" N ASP F 5 " pdb=" CA ASP F 5 " pdb=" C ASP F 5 " ideal model delta sigma weight residual 111.00 104.14 6.86 2.80e+00 1.28e-01 6.01e+00 angle pdb=" C ASP F 86 " pdb=" N ALA F 87 " pdb=" CA ALA F 87 " ideal model delta sigma weight residual 121.54 125.59 -4.05 1.91e+00 2.74e-01 4.50e+00 angle pdb=" C ASP H 86 " pdb=" N ALA H 87 " pdb=" CA ALA H 87 " ideal model delta sigma weight residual 121.54 125.55 -4.01 1.91e+00 2.74e-01 4.40e+00 angle pdb=" CA LEU E 11 " pdb=" CB LEU E 11 " pdb=" CG LEU E 11 " ideal model delta sigma weight residual 116.30 122.98 -6.68 3.50e+00 8.16e-02 3.64e+00 ... (remaining 14804 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 5423 17.73 - 35.46: 610 35.46 - 53.18: 164 53.18 - 70.91: 29 70.91 - 88.64: 11 Dihedral angle restraints: 6237 sinusoidal: 2299 harmonic: 3938 Sorted by residual: dihedral pdb=" CB CYS E 67 " pdb=" SG CYS E 67 " pdb=" SG CYS E 77 " pdb=" CB CYS E 77 " ideal model delta sinusoidal sigma weight residual -86.00 -126.95 40.95 1 1.00e+01 1.00e-02 2.35e+01 dihedral pdb=" SG CYS G 67 " pdb=" CB CYS G 77 " pdb=" SG CYS G 77 " pdb=" CA CYS G 77 " ideal model delta sinusoidal sigma weight residual -73.00 -9.75 -63.25 1 2.00e+01 2.50e-03 1.32e+01 dihedral pdb=" CA PHE A 571 " pdb=" C PHE A 571 " pdb=" N GLY A 572 " pdb=" CA GLY A 572 " ideal model delta harmonic sigma weight residual 180.00 163.00 17.00 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 6234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1080 0.028 - 0.055: 384 0.055 - 0.083: 156 0.083 - 0.111: 49 0.111 - 0.138: 6 Chirality restraints: 1675 Sorted by residual: chirality pdb=" CA ASP F 5 " pdb=" N ASP F 5 " pdb=" C ASP F 5 " pdb=" CB ASP F 5 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA PHE E 127 " pdb=" N PHE E 127 " pdb=" C PHE E 127 " pdb=" CB PHE E 127 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA VAL G 57 " pdb=" N VAL G 57 " pdb=" C VAL G 57 " pdb=" CB VAL G 57 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 ... (remaining 1672 not shown) Planarity restraints: 1810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 801 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.15e+00 pdb=" C GLY C 801 " 0.031 2.00e-02 2.50e+03 pdb=" O GLY C 801 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY C 802 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 808 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.04e+00 pdb=" C LEU D 808 " 0.030 2.00e-02 2.50e+03 pdb=" O LEU D 808 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL D 809 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 808 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.01e+00 pdb=" C LEU B 808 " -0.030 2.00e-02 2.50e+03 pdb=" O LEU B 808 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL B 809 " 0.010 2.00e-02 2.50e+03 ... (remaining 1807 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2097 2.76 - 3.30: 10797 3.30 - 3.83: 21152 3.83 - 4.37: 22364 4.37 - 4.90: 38366 Nonbonded interactions: 94776 Sorted by model distance: nonbonded pdb=" O HOH D 902 " pdb=" O HOH D 913 " model vdw 2.227 2.440 nonbonded pdb=" O HOH B 902 " pdb=" O HOH B 914 " model vdw 2.228 2.440 nonbonded pdb=" O ILE G 26 " pdb=" OG1 THR G 30 " model vdw 2.229 2.440 nonbonded pdb=" O ILE E 26 " pdb=" OG1 THR E 30 " model vdw 2.231 2.440 nonbonded pdb=" O HOH B 910 " pdb=" O HOH B 931 " model vdw 2.244 2.440 ... (remaining 94771 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 511 through 552 or resid 564 through 588 or resid 590 thro \ ugh 614 or resid 616 through 826)) selection = (chain 'B' and (resid 511 through 588 or resid 590 through 614 or resid 616 thro \ ugh 626 or resid 784 through 824 or (resid 825 and (name N or name CA or name C \ or name O or name CB )) or resid 826)) selection = (chain 'C' and (resid 511 through 552 or resid 564 through 588 or resid 590 thro \ ugh 614 or resid 616 through 826)) selection = (chain 'D' and (resid 511 through 588 or resid 590 through 614 or resid 616 thro \ ugh 626 or resid 784 through 824 or (resid 825 and (name N or name CA or name C \ or name O or name CB )) or resid 826)) } ncs_group { reference = (chain 'E' and (resid 5 through 130 or (resid 131 and (name N or name CA or name \ C or name O or name CB )) or resid 132 through 214)) selection = (chain 'F' and (resid 5 or (resid 6 and (name N or name CA or name C or name O o \ r name CB )) or resid 7 through 40 or (resid 41 and (name N or name CA or name C \ or name O or name CB )) or resid 42 through 214)) selection = (chain 'G' and (resid 5 through 130 or (resid 131 and (name N or name CA or name \ C or name O or name CB )) or resid 132 through 214)) selection = (chain 'H' and (resid 5 or (resid 6 and (name N or name CA or name C or name O o \ r name CB )) or resid 7 through 40 or (resid 41 and (name N or name CA or name C \ or name O or name CB )) or resid 42 through 214)) } 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=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.990 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: 10.660 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 37.000 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.060 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:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10931 Z= 0.135 Angle : 0.428 8.210 14809 Z= 0.241 Chirality : 0.035 0.138 1675 Planarity : 0.004 0.028 1810 Dihedral : 16.293 88.638 3691 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.54 % Allowed : 19.39 % Favored : 80.07 % 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: 3.17 (0.23), residues: 1339 helix: 3.07 (0.16), residues: 948 sheet: -2.38 (1.39), residues: 10 loop : -0.39 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 178 HIS 0.004 0.001 HIS F 205 PHE 0.020 0.001 PHE E 127 TYR 0.020 0.001 TYR C 549 ARG 0.002 0.000 ARG H 65 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 160 time to evaluate : 1.329 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 165 average time/residue: 1.1379 time to fit residues: 204.1360 Evaluate side-chains 164 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 158 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 11 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 586 GLN D 586 GLN H 72 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.0676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10931 Z= 0.208 Angle : 0.477 6.012 14809 Z= 0.269 Chirality : 0.037 0.135 1675 Planarity : 0.004 0.041 1810 Dihedral : 4.945 56.641 1479 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.59 % Allowed : 16.98 % Favored : 80.43 % 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: 3.74 (0.23), residues: 1339 helix: 3.53 (0.16), residues: 950 sheet: -0.02 (1.11), residues: 30 loop : -0.39 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 606 HIS 0.005 0.001 HIS F 205 PHE 0.019 0.002 PHE E 127 TYR 0.020 0.002 TYR C 549 ARG 0.002 0.000 ARG D 594 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 160 time to evaluate : 1.176 Fit side-chains revert: symmetry clash REVERT: D 825 MET cc_start: 0.4653 (tpp) cc_final: 0.4407 (ptm) REVERT: F 78 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7453 (ttpt) REVERT: H 65 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7178 (mtp-110) REVERT: H 130 THR cc_start: 0.7329 (t) cc_final: 0.6994 (m) outliers start: 29 outliers final: 17 residues processed: 173 average time/residue: 1.1282 time to fit residues: 212.3303 Evaluate side-chains 170 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 151 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 4.9990 chunk 37 optimal weight: 0.2980 chunk 99 optimal weight: 5.9990 chunk 81 optimal weight: 0.0670 chunk 33 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 129 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 586 GLN D 586 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.0652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10931 Z= 0.146 Angle : 0.421 6.148 14809 Z= 0.237 Chirality : 0.035 0.134 1675 Planarity : 0.003 0.029 1810 Dihedral : 4.486 57.185 1476 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.68 % Allowed : 17.34 % Favored : 79.98 % 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: 3.95 (0.23), residues: 1339 helix: 3.71 (0.16), residues: 954 sheet: -1.80 (1.44), residues: 10 loop : -0.38 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 178 HIS 0.004 0.001 HIS H 205 PHE 0.020 0.001 PHE E 127 TYR 0.017 0.001 TYR C 549 ARG 0.001 0.000 ARG H 65 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 166 time to evaluate : 1.268 Fit side-chains REVERT: E 99 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.6993 (mpp80) REVERT: E 131 ARG cc_start: 0.6108 (OUTLIER) cc_final: 0.5577 (mmp-170) REVERT: G 131 ARG cc_start: 0.5852 (OUTLIER) cc_final: 0.5121 (mtp180) REVERT: H 65 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7199 (mtp-110) REVERT: H 130 THR cc_start: 0.7382 (t) cc_final: 0.6979 (m) outliers start: 30 outliers final: 9 residues processed: 182 average time/residue: 1.0821 time to fit residues: 215.0217 Evaluate side-chains 172 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 159 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 78 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 586 GLN D 586 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10931 Z= 0.295 Angle : 0.542 6.393 14809 Z= 0.307 Chirality : 0.041 0.141 1675 Planarity : 0.004 0.055 1810 Dihedral : 4.989 59.186 1476 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.95 % Allowed : 16.44 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.44 (0.23), residues: 1339 helix: 3.26 (0.16), residues: 948 sheet: -0.62 (0.91), residues: 40 loop : -0.27 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 606 HIS 0.006 0.001 HIS F 205 PHE 0.019 0.003 PHE E 127 TYR 0.026 0.003 TYR H 181 ARG 0.004 0.001 ARG D 594 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 164 time to evaluate : 1.245 Fit side-chains REVERT: B 570 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7899 (mt-10) REVERT: B 813 GLU cc_start: 0.8345 (tt0) cc_final: 0.8072 (tt0) REVERT: D 570 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7883 (mt-10) REVERT: D 813 GLU cc_start: 0.8459 (tt0) cc_final: 0.8110 (tt0) REVERT: E 99 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6998 (mpp80) REVERT: E 131 ARG cc_start: 0.6254 (OUTLIER) cc_final: 0.5824 (mmp-170) REVERT: G 131 ARG cc_start: 0.6038 (OUTLIER) cc_final: 0.5450 (mmp-170) REVERT: F 78 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7446 (ttpt) REVERT: H 65 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7116 (mtp-110) REVERT: H 130 THR cc_start: 0.7376 (t) cc_final: 0.7011 (m) outliers start: 33 outliers final: 14 residues processed: 178 average time/residue: 1.1235 time to fit residues: 217.5210 Evaluate side-chains 176 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 157 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 114 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 586 GLN D 586 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10931 Z= 0.187 Angle : 0.458 6.517 14809 Z= 0.259 Chirality : 0.037 0.134 1675 Planarity : 0.003 0.035 1810 Dihedral : 4.679 58.229 1474 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.59 % Allowed : 16.89 % Favored : 80.52 % 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: 3.69 (0.23), residues: 1339 helix: 3.48 (0.16), residues: 952 sheet: -0.12 (1.07), residues: 30 loop : -0.41 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 178 HIS 0.004 0.001 HIS F 205 PHE 0.019 0.002 PHE E 127 TYR 0.016 0.002 TYR C 549 ARG 0.002 0.000 ARG D 594 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 166 time to evaluate : 1.225 Fit side-chains REVERT: B 570 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7783 (mt-10) REVERT: B 813 GLU cc_start: 0.8293 (tt0) cc_final: 0.7951 (tt0) REVERT: B 825 MET cc_start: 0.4841 (tpp) cc_final: 0.4306 (tpp) REVERT: D 570 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7773 (mt-10) REVERT: D 813 GLU cc_start: 0.8405 (tt0) cc_final: 0.8016 (tt0) REVERT: E 99 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.6992 (mpp80) REVERT: E 131 ARG cc_start: 0.6186 (OUTLIER) cc_final: 0.5740 (mmp-170) REVERT: G 56 GLU cc_start: 0.5714 (OUTLIER) cc_final: 0.4493 (tp30) REVERT: G 131 ARG cc_start: 0.6004 (OUTLIER) cc_final: 0.5391 (mmp-170) REVERT: F 78 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7452 (ttpt) REVERT: H 130 THR cc_start: 0.7362 (t) cc_final: 0.7000 (m) outliers start: 29 outliers final: 14 residues processed: 181 average time/residue: 1.1173 time to fit residues: 220.3573 Evaluate side-chains 179 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 160 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 586 GLN D 586 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10931 Z= 0.186 Angle : 0.458 6.639 14809 Z= 0.258 Chirality : 0.037 0.136 1675 Planarity : 0.003 0.036 1810 Dihedral : 4.665 58.801 1474 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.77 % Allowed : 16.53 % Favored : 80.70 % 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: 3.71 (0.23), residues: 1339 helix: 3.50 (0.16), residues: 952 sheet: -0.12 (1.08), residues: 30 loop : -0.38 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 178 HIS 0.004 0.001 HIS H 205 PHE 0.019 0.002 PHE E 127 TYR 0.017 0.002 TYR H 181 ARG 0.002 0.000 ARG H 65 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 164 time to evaluate : 2.241 Fit side-chains REVERT: B 570 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7802 (mt-10) REVERT: B 813 GLU cc_start: 0.8308 (tt0) cc_final: 0.7973 (tt0) REVERT: B 825 MET cc_start: 0.4849 (tpp) cc_final: 0.4373 (tpp) REVERT: D 570 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7793 (mt-10) REVERT: D 813 GLU cc_start: 0.8344 (tt0) cc_final: 0.8001 (tt0) REVERT: E 99 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.7034 (mpp80) REVERT: E 131 ARG cc_start: 0.6207 (OUTLIER) cc_final: 0.5736 (mmp-170) REVERT: G 56 GLU cc_start: 0.5849 (OUTLIER) cc_final: 0.4582 (tp30) REVERT: G 131 ARG cc_start: 0.6007 (OUTLIER) cc_final: 0.5428 (mmp-170) REVERT: F 78 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7453 (ttpt) REVERT: H 130 THR cc_start: 0.7367 (t) cc_final: 0.7004 (m) outliers start: 31 outliers final: 16 residues processed: 181 average time/residue: 1.1142 time to fit residues: 219.5421 Evaluate side-chains 178 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 157 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 586 GLN D 586 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10931 Z= 0.168 Angle : 0.444 6.603 14809 Z= 0.250 Chirality : 0.036 0.136 1675 Planarity : 0.003 0.031 1810 Dihedral : 4.583 58.705 1474 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.41 % Allowed : 16.44 % Favored : 81.14 % 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: 3.80 (0.23), residues: 1339 helix: 3.56 (0.16), residues: 954 sheet: -1.48 (1.43), residues: 10 loop : -0.32 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 178 HIS 0.004 0.001 HIS H 205 PHE 0.019 0.002 PHE E 127 TYR 0.016 0.002 TYR C 549 ARG 0.002 0.000 ARG H 65 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 162 time to evaluate : 1.227 Fit side-chains revert: symmetry clash REVERT: B 570 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7802 (mt-10) REVERT: B 813 GLU cc_start: 0.8294 (tt0) cc_final: 0.7956 (tt0) REVERT: D 570 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7811 (mt-10) REVERT: D 813 GLU cc_start: 0.8332 (tt0) cc_final: 0.7986 (tt0) REVERT: E 99 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6977 (mpp80) REVERT: E 131 ARG cc_start: 0.6195 (OUTLIER) cc_final: 0.5721 (mmp-170) REVERT: G 56 GLU cc_start: 0.5832 (OUTLIER) cc_final: 0.4582 (tp30) REVERT: G 131 ARG cc_start: 0.5971 (OUTLIER) cc_final: 0.5381 (mmp-170) REVERT: F 78 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7459 (ttpt) REVERT: H 130 THR cc_start: 0.7349 (t) cc_final: 0.6971 (m) outliers start: 27 outliers final: 18 residues processed: 175 average time/residue: 1.1564 time to fit residues: 220.2496 Evaluate side-chains 180 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 157 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 7.9990 chunk 38 optimal weight: 0.3980 chunk 24 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 586 GLN D 586 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10931 Z= 0.219 Angle : 0.487 6.712 14809 Z= 0.274 Chirality : 0.038 0.136 1675 Planarity : 0.004 0.041 1810 Dihedral : 4.729 59.715 1474 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.41 % Allowed : 16.71 % Favored : 80.88 % 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: 3.62 (0.23), residues: 1339 helix: 3.40 (0.15), residues: 950 sheet: -0.05 (1.08), residues: 30 loop : -0.32 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 178 HIS 0.005 0.001 HIS F 205 PHE 0.019 0.002 PHE E 127 TYR 0.020 0.002 TYR H 181 ARG 0.002 0.000 ARG E 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 162 time to evaluate : 1.466 Fit side-chains revert: symmetry clash REVERT: B 570 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7947 (mt-10) REVERT: B 813 GLU cc_start: 0.8324 (tt0) cc_final: 0.7995 (tt0) REVERT: D 570 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7935 (mt-10) REVERT: D 813 GLU cc_start: 0.8352 (tt0) cc_final: 0.8023 (tt0) REVERT: E 99 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6963 (mpp80) REVERT: E 131 ARG cc_start: 0.6268 (OUTLIER) cc_final: 0.5848 (mmp-170) REVERT: G 56 GLU cc_start: 0.5853 (OUTLIER) cc_final: 0.4584 (tp30) REVERT: G 131 ARG cc_start: 0.6008 (OUTLIER) cc_final: 0.5488 (mmp-170) REVERT: F 78 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7454 (ttpt) REVERT: H 130 THR cc_start: 0.7341 (t) cc_final: 0.6966 (m) outliers start: 27 outliers final: 19 residues processed: 174 average time/residue: 1.1270 time to fit residues: 213.2013 Evaluate side-chains 182 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 158 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain D residue 825 MET Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.4980 chunk 121 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10931 Z= 0.216 Angle : 0.488 6.830 14809 Z= 0.275 Chirality : 0.038 0.140 1675 Planarity : 0.004 0.042 1810 Dihedral : 4.730 59.526 1474 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.50 % Allowed : 16.53 % Favored : 80.97 % 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: 3.59 (0.23), residues: 1339 helix: 3.38 (0.16), residues: 952 sheet: -0.04 (1.08), residues: 30 loop : -0.38 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 178 HIS 0.004 0.001 HIS F 205 PHE 0.019 0.002 PHE E 127 TYR 0.018 0.002 TYR H 181 ARG 0.002 0.000 ARG D 594 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 161 time to evaluate : 1.244 Fit side-chains revert: symmetry clash REVERT: B 570 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7923 (mt-10) REVERT: B 813 GLU cc_start: 0.8317 (tt0) cc_final: 0.7983 (tt0) REVERT: D 570 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7927 (mt-10) REVERT: D 813 GLU cc_start: 0.8347 (tt0) cc_final: 0.7995 (tt0) REVERT: E 99 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6973 (mpp80) REVERT: E 131 ARG cc_start: 0.6207 (OUTLIER) cc_final: 0.5754 (mmp-170) REVERT: G 56 GLU cc_start: 0.5847 (OUTLIER) cc_final: 0.4578 (tp30) REVERT: G 131 ARG cc_start: 0.6049 (OUTLIER) cc_final: 0.5530 (mmp-170) REVERT: F 78 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7452 (ttpt) REVERT: H 130 THR cc_start: 0.7341 (t) cc_final: 0.6967 (m) outliers start: 28 outliers final: 19 residues processed: 174 average time/residue: 1.1556 time to fit residues: 218.9626 Evaluate side-chains 182 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 158 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain D residue 825 MET Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 chunk 111 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 586 GLN D 586 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10931 Z= 0.310 Angle : 0.565 6.968 14809 Z= 0.317 Chirality : 0.041 0.143 1675 Planarity : 0.004 0.054 1810 Dihedral : 4.978 59.570 1474 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.68 % Allowed : 16.44 % Favored : 80.88 % 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: 3.25 (0.23), residues: 1339 helix: 3.12 (0.15), residues: 948 sheet: -0.04 (1.08), residues: 30 loop : -0.43 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 606 HIS 0.006 0.001 HIS H 205 PHE 0.019 0.003 PHE E 127 TYR 0.024 0.003 TYR H 181 ARG 0.003 0.001 ARG D 594 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 157 time to evaluate : 1.131 Fit side-chains revert: symmetry clash REVERT: B 570 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7962 (mt-10) REVERT: B 813 GLU cc_start: 0.8364 (tt0) cc_final: 0.8028 (tt0) REVERT: D 570 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7950 (mt-10) REVERT: D 813 GLU cc_start: 0.8361 (tt0) cc_final: 0.8080 (tt0) REVERT: E 99 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.6993 (mpp80) REVERT: E 131 ARG cc_start: 0.6253 (OUTLIER) cc_final: 0.5855 (mmp-170) REVERT: G 56 GLU cc_start: 0.5699 (OUTLIER) cc_final: 0.4480 (tp30) REVERT: G 131 ARG cc_start: 0.6023 (OUTLIER) cc_final: 0.5509 (mmp-170) REVERT: F 78 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7437 (ttpt) REVERT: F 130 THR cc_start: 0.7279 (t) cc_final: 0.6819 (m) REVERT: H 130 THR cc_start: 0.7333 (t) cc_final: 0.6963 (m) outliers start: 30 outliers final: 17 residues processed: 171 average time/residue: 1.1610 time to fit residues: 215.7322 Evaluate side-chains 179 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 157 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 586 GLN D 586 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.192358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.140919 restraints weight = 31148.170| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 4.51 r_work: 0.3076 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10931 Z= 0.174 Angle : 0.462 6.870 14809 Z= 0.259 Chirality : 0.037 0.136 1675 Planarity : 0.003 0.033 1810 Dihedral : 4.723 58.963 1474 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.32 % Allowed : 16.89 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.65 (0.23), residues: 1339 helix: 3.45 (0.16), residues: 952 sheet: -0.10 (1.06), residues: 30 loop : -0.42 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 178 HIS 0.004 0.001 HIS F 205 PHE 0.019 0.002 PHE E 127 TYR 0.017 0.002 TYR C 549 ARG 0.002 0.000 ARG A 599 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4164.53 seconds wall clock time: 75 minutes 27.47 seconds (4527.47 seconds total)