Starting phenix.real_space_refine on Wed Sep 25 14:25:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fps_29369/09_2024/8fps_29369.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fps_29369/09_2024/8fps_29369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fps_29369/09_2024/8fps_29369.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fps_29369/09_2024/8fps_29369.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fps_29369/09_2024/8fps_29369.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fps_29369/09_2024/8fps_29369.cif" } resolution = 2.38 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 74 5.16 5 Cl 4 4.86 5 C 6884 2.51 5 N 1662 2.21 5 O 1978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10602 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1159 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 146, 1147 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 146, 1147 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 141} 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: 1165 Chain: "B" Number of atoms: 1190 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 151, 1184 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 146} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 151, 1184 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 146} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 1209 Chain: "C" Number of atoms: 1159 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 146, 1147 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 146, 1147 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 141} 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: 1165 Chain: "D" Number of atoms: 1190 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 151, 1184 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 146} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 151, 1184 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 146} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 1209 Chain: "E" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1435 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 183} 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: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1435 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 183} 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: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1439 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 183} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1439 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 183} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "E" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "G" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "F" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "H" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} 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=0.50 ... (10 atoms not shown) pdb=" SG BCYS 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: 8.93, per 1000 atoms: 0.84 Number of scatterers: 10602 At special positions: 0 Unit cell: (112.203, 110.565, 86.814, 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 4 17.00 S 74 16.00 O 1978 8.00 N 1662 7.00 C 6884 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 - 3.00 Amino acid : True - 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: 2.42 Conformation dependent library (CDL) restraints added in 1.9 seconds 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2464 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 4 sheets defined 74.8% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 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 551 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 624 Processing helix chain 'B' and resid 788 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 551 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 791 Processing helix chain 'C' and resid 792 through 826 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 624 Processing helix chain 'D' and resid 788 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 70 through 74 removed outlier: 4.170A pdb=" N PHE E 73 " --> pdb=" O GLU E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 105 removed outlier: 3.611A pdb=" N TYR E 96 " --> pdb=" O ASP E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 128 Processing helix chain 'E' and resid 132 through 160 removed outlier: 3.699A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 211 Processing helix chain 'G' and resid 6 through 30 Processing helix chain 'G' and resid 70 through 74 removed outlier: 4.159A pdb=" N PHE G 73 " --> pdb=" O GLU G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 105 removed outlier: 3.570A pdb=" N TYR G 96 " --> pdb=" O ASP G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 128 removed outlier: 3.842A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 160 removed outlier: 3.713A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 212 Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 92 through 105 Processing helix chain 'F' and resid 105 through 129 removed outlier: 3.524A pdb=" N ILE F 109 " --> pdb=" O SER F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 162 removed outlier: 3.633A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 212 Processing helix chain 'H' and resid 6 through 30 Processing helix chain 'H' and resid 92 through 105 Processing helix chain 'H' and resid 105 through 129 removed outlier: 3.508A pdb=" N ILE H 109 " --> pdb=" O SER H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 162 removed outlier: 3.651A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 212 Processing sheet with id=AA1, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AA2, first strand: chain 'G' and resid 77 through 79 Processing sheet with id=AA3, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AA4, first strand: chain 'H' and resid 77 through 79 855 hydrogen bonds defined for protein. 2468 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: 3.03 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3146 1.34 - 1.46: 2871 1.46 - 1.58: 4583 1.58 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 10712 Sorted by residual: bond pdb=" N GLY B 588 " pdb=" CA GLY B 588 " ideal model delta sigma weight residual 1.447 1.454 -0.008 1.09e-02 8.42e+03 5.19e-01 bond pdb=" C VAL C 792 " pdb=" O VAL C 792 " ideal model delta sigma weight residual 1.231 1.241 -0.010 1.51e-02 4.39e+03 3.97e-01 bond pdb=" N GLY D 588 " pdb=" CA GLY D 588 " ideal model delta sigma weight residual 1.447 1.453 -0.007 1.09e-02 8.42e+03 3.96e-01 bond pdb=" C PHE D 607 " pdb=" O PHE D 607 " ideal model delta sigma weight residual 1.236 1.244 -0.007 1.15e-02 7.56e+03 3.80e-01 bond pdb=" C VAL A 792 " pdb=" O VAL A 792 " ideal model delta sigma weight residual 1.235 1.244 -0.008 1.45e-02 4.76e+03 3.42e-01 ... (remaining 10707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.94: 14102 0.94 - 1.88: 334 1.88 - 2.82: 45 2.82 - 3.76: 15 3.76 - 4.70: 10 Bond angle restraints: 14506 Sorted by residual: angle pdb=" CA TYR C 523 " pdb=" CB TYR C 523 " pdb=" CG TYR C 523 " ideal model delta sigma weight residual 113.90 117.55 -3.65 1.80e+00 3.09e-01 4.12e+00 angle pdb=" CA TYR A 523 " pdb=" CB TYR A 523 " pdb=" CG TYR A 523 " ideal model delta sigma weight residual 113.90 117.19 -3.29 1.80e+00 3.09e-01 3.35e+00 angle pdb=" CA GLU A 550 " pdb=" CB GLU A 550 " pdb=" CG GLU A 550 " ideal model delta sigma weight residual 114.10 117.72 -3.62 2.00e+00 2.50e-01 3.27e+00 angle pdb=" CA GLU C 550 " pdb=" CB GLU C 550 " pdb=" CG GLU C 550 " ideal model delta sigma weight residual 114.10 117.42 -3.32 2.00e+00 2.50e-01 2.76e+00 angle pdb=" N PHE F 107 " pdb=" CA PHE F 107 " pdb=" C PHE F 107 " ideal model delta sigma weight residual 109.81 113.32 -3.51 2.21e+00 2.05e-01 2.52e+00 ... (remaining 14501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5356 17.93 - 35.86: 551 35.86 - 53.79: 144 53.79 - 71.72: 36 71.72 - 89.65: 9 Dihedral angle restraints: 6096 sinusoidal: 2246 harmonic: 3850 Sorted by residual: dihedral pdb=" CB CYS H 40 " pdb=" SG CYS H 40 " pdb=" SG CYS H 68 " pdb=" CB CYS H 68 " ideal model delta sinusoidal sigma weight residual -86.00 -131.23 45.23 1 1.00e+01 1.00e-02 2.84e+01 dihedral pdb=" CB CYS F 40 " pdb=" SG CYS F 40 " pdb=" SG CYS F 68 " pdb=" CB CYS F 68 " ideal model delta sinusoidal sigma weight residual -86.00 -131.16 45.16 1 1.00e+01 1.00e-02 2.83e+01 dihedral pdb=" CB GLU E 90 " pdb=" CG GLU E 90 " pdb=" CD GLU E 90 " pdb=" OE1 GLU E 90 " ideal model delta sinusoidal sigma weight residual 0.00 89.65 -89.65 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 6093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 969 0.021 - 0.043: 327 0.043 - 0.064: 223 0.064 - 0.085: 90 0.085 - 0.107: 29 Chirality restraints: 1638 Sorted by residual: chirality pdb=" CA PHE H 107 " pdb=" N PHE H 107 " pdb=" C PHE H 107 " pdb=" CB PHE H 107 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.84e-01 chirality pdb=" CA PRO A 520 " pdb=" N PRO A 520 " pdb=" C PRO A 520 " pdb=" CB PRO A 520 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.82e-01 chirality pdb=" CA PRO D 520 " pdb=" N PRO D 520 " pdb=" C PRO D 520 " pdb=" CB PRO D 520 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.81e-01 ... (remaining 1635 not shown) Planarity restraints: 1766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE G 107 " -0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO G 108 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO G 108 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO G 108 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 60 " -0.008 2.00e-02 2.50e+03 1.01e-02 1.53e+00 pdb=" CG HIS E 60 " 0.022 2.00e-02 2.50e+03 pdb=" ND1 HIS E 60 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 HIS E 60 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 HIS E 60 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS E 60 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE E 107 " 0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO E 108 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO E 108 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 108 " 0.017 5.00e-02 4.00e+02 ... (remaining 1763 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1396 2.75 - 3.29: 10427 3.29 - 3.83: 19341 3.83 - 4.36: 20648 4.36 - 4.90: 36556 Nonbonded interactions: 88368 Sorted by model distance: nonbonded pdb=" OG1 THR G 30 " pdb=" OG SER G 179 " model vdw 2.215 3.040 nonbonded pdb=" OG1 THR E 30 " pdb=" OG SER E 179 " model vdw 2.223 3.040 nonbonded pdb=" O SER E 105 " pdb=" OG SER E 105 " model vdw 2.232 3.040 nonbonded pdb=" O SER G 105 " pdb=" OG SER G 105 " model vdw 2.233 3.040 nonbonded pdb=" O HOH B 926 " pdb=" O HOH D 925 " model vdw 2.243 3.040 ... (remaining 88363 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 511 or (resid 512 and (name N or name CA or name C or name \ O or name CB )) or resid 513 through 588 or resid 590 through 614 or resid 616 \ through 625 or resid 784 through 826)) selection = (chain 'B' and (resid 511 through 552 or resid 566 through 588 or resid 590 thro \ ugh 614 or resid 616 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 or (resid 512 and (name N or name CA or name C or name \ O or name CB )) or resid 513 through 588 or resid 590 through 614 or resid 616 \ through 625 or resid 784 through 826)) selection = (chain 'D' and (resid 511 through 552 or resid 566 through 588 or resid 590 thro \ ugh 614 or resid 616 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 212 or resid 401)) 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 212 or resid 401)) 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 212 or resid 401)) 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 212 or resid 401)) } 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=0.50 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: 19.160 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: 0.140 Check model and map are aligned: 0.000 Set scattering table: 0.060 Process input model: 28.590 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 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 0.022 10712 Z= 0.115 Angle : 0.371 4.700 14506 Z= 0.209 Chirality : 0.033 0.107 1638 Planarity : 0.002 0.031 1766 Dihedral : 16.267 89.649 3608 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.01 % Allowed : 19.20 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.11 (0.23), residues: 1308 helix: 3.82 (0.15), residues: 930 sheet: 1.09 (0.82), residues: 40 loop : -0.50 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 64 HIS 0.012 0.001 HIS E 60 PHE 0.010 0.001 PHE G 107 TYR 0.021 0.001 TYR A 523 ARG 0.001 0.000 ARG G 209 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 145 time to evaluate : 1.212 Fit side-chains REVERT: E 11 LEU cc_start: 0.7891 (tm) cc_final: 0.7600 (tp) REVERT: E 97 PHE cc_start: 0.6303 (t80) cc_final: 0.6001 (t80) REVERT: G 97 PHE cc_start: 0.6345 (t80) cc_final: 0.6012 (t80) outliers start: 10 outliers final: 9 residues processed: 155 average time/residue: 1.0794 time to fit residues: 182.2394 Evaluate side-chains 154 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 145 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain F residue 120 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 60 HIS E 132 HIS G 132 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10712 Z= 0.209 Angle : 0.465 4.603 14506 Z= 0.263 Chirality : 0.037 0.121 1638 Planarity : 0.003 0.035 1766 Dihedral : 4.752 51.862 1447 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.37 % Allowed : 18.28 % Favored : 80.35 % 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: 4.03 (0.23), residues: 1308 helix: 3.78 (0.16), residues: 928 sheet: 0.03 (0.68), residues: 60 loop : -0.44 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 578 HIS 0.009 0.001 HIS E 60 PHE 0.014 0.002 PHE G 107 TYR 0.016 0.002 TYR C 523 ARG 0.004 0.000 ARG G 209 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 157 time to evaluate : 1.095 Fit side-chains outliers start: 14 outliers final: 5 residues processed: 164 average time/residue: 1.0871 time to fit residues: 193.2584 Evaluate side-chains 152 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 147 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 8.9990 chunk 36 optimal weight: 0.0980 chunk 98 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 E 132 HIS G 132 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10712 Z= 0.213 Angle : 0.467 4.549 14506 Z= 0.264 Chirality : 0.037 0.121 1638 Planarity : 0.003 0.036 1766 Dihedral : 4.082 40.946 1437 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.55 % Allowed : 18.46 % 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: 3.79 (0.23), residues: 1308 helix: 3.62 (0.16), residues: 928 sheet: 0.63 (0.78), residues: 40 loop : -0.67 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 578 HIS 0.006 0.001 HIS E 205 PHE 0.014 0.002 PHE G 107 TYR 0.018 0.002 TYR A 523 ARG 0.004 0.000 ARG G 209 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 164 time to evaluate : 1.105 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 171 average time/residue: 1.1680 time to fit residues: 215.9613 Evaluate side-chains 163 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 155 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 125 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 E 132 HIS G 132 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10712 Z= 0.140 Angle : 0.404 4.614 14506 Z= 0.229 Chirality : 0.035 0.111 1638 Planarity : 0.003 0.035 1766 Dihedral : 3.595 25.022 1435 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.83 % Allowed : 17.82 % Favored : 80.35 % 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: 4.10 (0.23), residues: 1308 helix: 3.88 (0.16), residues: 930 sheet: 0.77 (0.80), residues: 40 loop : -0.66 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 178 HIS 0.004 0.001 HIS E 205 PHE 0.010 0.001 PHE E 107 TYR 0.019 0.001 TYR C 523 ARG 0.002 0.000 ARG G 209 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 168 time to evaluate : 1.177 Fit side-chains REVERT: B 825 MET cc_start: 0.3154 (OUTLIER) cc_final: 0.2534 (tpp) REVERT: D 825 MET cc_start: 0.3204 (OUTLIER) cc_final: 0.2606 (tpp) REVERT: E 11 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7590 (tp) REVERT: E 90 GLU cc_start: 0.1034 (OUTLIER) cc_final: -0.0432 (pm20) REVERT: E 97 PHE cc_start: 0.6363 (t80) cc_final: 0.5965 (t80) REVERT: G 90 GLU cc_start: 0.0951 (OUTLIER) cc_final: -0.0488 (pm20) REVERT: G 97 PHE cc_start: 0.6333 (t80) cc_final: 0.5898 (t80) outliers start: 20 outliers final: 6 residues processed: 175 average time/residue: 1.0907 time to fit residues: 206.9600 Evaluate side-chains 170 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 159 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain D residue 825 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS G 132 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10712 Z= 0.227 Angle : 0.474 4.532 14506 Z= 0.268 Chirality : 0.037 0.122 1638 Planarity : 0.003 0.037 1766 Dihedral : 3.794 16.246 1434 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.01 % Allowed : 18.46 % Favored : 79.52 % 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: 3.71 (0.23), residues: 1308 helix: 3.56 (0.16), residues: 932 sheet: 0.59 (0.81), residues: 40 loop : -0.73 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 578 HIS 0.006 0.001 HIS E 205 PHE 0.025 0.002 PHE E 127 TYR 0.020 0.002 TYR A 523 ARG 0.004 0.000 ARG G 209 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 160 time to evaluate : 1.125 Fit side-chains REVERT: A 550 GLU cc_start: 0.6912 (pp20) cc_final: 0.6693 (pm20) REVERT: B 825 MET cc_start: 0.3206 (OUTLIER) cc_final: 0.2562 (tpp) REVERT: D 825 MET cc_start: 0.3145 (OUTLIER) cc_final: 0.2503 (tpp) REVERT: E 58 MET cc_start: 0.6542 (OUTLIER) cc_final: 0.6337 (tpt) REVERT: E 90 GLU cc_start: 0.1012 (OUTLIER) cc_final: -0.0420 (pm20) REVERT: E 120 LEU cc_start: 0.7902 (tp) cc_final: 0.7612 (mt) outliers start: 22 outliers final: 9 residues processed: 170 average time/residue: 1.0971 time to fit residues: 202.7257 Evaluate side-chains 167 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 154 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain D residue 825 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain G residue 10 MET Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS G 132 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10712 Z= 0.143 Angle : 0.411 5.084 14506 Z= 0.233 Chirality : 0.035 0.121 1638 Planarity : 0.003 0.038 1766 Dihedral : 3.599 16.807 1434 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.46 % Allowed : 18.65 % Favored : 79.89 % 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: 4.05 (0.23), residues: 1308 helix: 3.82 (0.16), residues: 934 sheet: 0.73 (0.81), residues: 40 loop : -0.67 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 178 HIS 0.004 0.001 HIS E 205 PHE 0.018 0.001 PHE E 127 TYR 0.019 0.001 TYR C 523 ARG 0.002 0.000 ARG G 209 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 168 time to evaluate : 1.105 Fit side-chains REVERT: B 514 VAL cc_start: 0.7541 (t) cc_final: 0.7284 (p) REVERT: B 825 MET cc_start: 0.3145 (OUTLIER) cc_final: 0.2524 (tpp) REVERT: D 825 MET cc_start: 0.3184 (OUTLIER) cc_final: 0.2566 (tpp) REVERT: E 11 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7589 (tp) REVERT: E 58 MET cc_start: 0.6454 (OUTLIER) cc_final: 0.6201 (tpt) REVERT: E 90 GLU cc_start: 0.0741 (OUTLIER) cc_final: -0.0508 (pm20) REVERT: E 97 PHE cc_start: 0.6335 (t80) cc_final: 0.5901 (t80) REVERT: G 97 PHE cc_start: 0.6319 (t80) cc_final: 0.5864 (t80) outliers start: 16 outliers final: 5 residues processed: 175 average time/residue: 1.0824 time to fit residues: 205.6316 Evaluate side-chains 172 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 162 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain D residue 825 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 66 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 0.9980 chunk 14 optimal weight: 8.9990 chunk 71 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 105 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 57 optimal weight: 0.2980 chunk 77 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS G 132 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10712 Z= 0.129 Angle : 0.400 7.184 14506 Z= 0.225 Chirality : 0.035 0.123 1638 Planarity : 0.003 0.039 1766 Dihedral : 3.498 16.137 1434 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.55 % Allowed : 18.74 % Favored : 79.71 % 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: 4.23 (0.23), residues: 1308 helix: 3.96 (0.16), residues: 934 sheet: 0.82 (0.82), residues: 40 loop : -0.63 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 178 HIS 0.004 0.001 HIS H 205 PHE 0.016 0.001 PHE E 127 TYR 0.019 0.001 TYR C 523 ARG 0.002 0.000 ARG G 209 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 163 time to evaluate : 1.158 Fit side-chains REVERT: D 825 MET cc_start: 0.3308 (OUTLIER) cc_final: 0.2681 (tpp) REVERT: E 11 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7596 (tp) REVERT: E 90 GLU cc_start: 0.0677 (OUTLIER) cc_final: -0.0582 (pm20) REVERT: E 97 PHE cc_start: 0.6328 (t80) cc_final: 0.5905 (t80) REVERT: G 97 PHE cc_start: 0.6300 (t80) cc_final: 0.5875 (t80) outliers start: 17 outliers final: 5 residues processed: 171 average time/residue: 1.1150 time to fit residues: 206.5949 Evaluate side-chains 162 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 154 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 825 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 113 optimal weight: 0.6980 chunk 120 optimal weight: 6.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS G 132 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10712 Z= 0.204 Angle : 0.462 6.345 14506 Z= 0.259 Chirality : 0.037 0.118 1638 Planarity : 0.003 0.038 1766 Dihedral : 3.713 15.669 1434 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.10 % Allowed : 19.29 % Favored : 79.62 % 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: 3.90 (0.23), residues: 1308 helix: 3.69 (0.16), residues: 932 sheet: 0.69 (0.82), residues: 40 loop : -0.64 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 578 HIS 0.006 0.001 HIS E 205 PHE 0.015 0.002 PHE E 127 TYR 0.013 0.002 TYR G 181 ARG 0.003 0.000 ARG G 209 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 156 time to evaluate : 1.118 Fit side-chains REVERT: D 825 MET cc_start: 0.3143 (OUTLIER) cc_final: 0.2509 (tpp) REVERT: E 90 GLU cc_start: 0.0838 (OUTLIER) cc_final: -0.0440 (pm20) REVERT: E 97 PHE cc_start: 0.6318 (t80) cc_final: 0.5893 (t80) REVERT: G 97 PHE cc_start: 0.6316 (t80) cc_final: 0.5880 (t80) outliers start: 12 outliers final: 7 residues processed: 162 average time/residue: 1.1202 time to fit residues: 196.5340 Evaluate side-chains 164 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 155 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 825 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS G 132 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10712 Z= 0.190 Angle : 0.452 6.285 14506 Z= 0.254 Chirality : 0.036 0.116 1638 Planarity : 0.003 0.038 1766 Dihedral : 3.715 15.619 1434 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.01 % Allowed : 19.29 % Favored : 79.71 % 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: 3.88 (0.23), residues: 1308 helix: 3.66 (0.16), residues: 932 sheet: 0.63 (0.84), residues: 40 loop : -0.61 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 578 HIS 0.006 0.001 HIS E 205 PHE 0.015 0.002 PHE C 546 TYR 0.013 0.002 TYR G 181 ARG 0.002 0.000 ARG G 209 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 156 time to evaluate : 1.173 Fit side-chains REVERT: D 825 MET cc_start: 0.3189 (OUTLIER) cc_final: 0.2572 (tpp) REVERT: E 90 GLU cc_start: 0.0822 (OUTLIER) cc_final: -0.0447 (pm20) REVERT: E 120 LEU cc_start: 0.7950 (tp) cc_final: 0.7658 (mt) REVERT: G 97 PHE cc_start: 0.6335 (t80) cc_final: 0.5900 (t80) outliers start: 11 outliers final: 8 residues processed: 161 average time/residue: 1.1452 time to fit residues: 200.2393 Evaluate side-chains 166 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 156 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 825 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS G 132 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10712 Z= 0.242 Angle : 0.495 6.456 14506 Z= 0.277 Chirality : 0.038 0.123 1638 Planarity : 0.003 0.038 1766 Dihedral : 3.857 16.463 1434 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.01 % Allowed : 19.38 % Favored : 79.62 % 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: 3.64 (0.23), residues: 1308 helix: 3.47 (0.16), residues: 932 sheet: 0.52 (0.84), residues: 40 loop : -0.65 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 578 HIS 0.007 0.001 HIS E 205 PHE 0.016 0.002 PHE C 546 TYR 0.016 0.002 TYR H 181 ARG 0.003 0.000 ARG G 209 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 161 time to evaluate : 1.286 Fit side-chains REVERT: A 550 GLU cc_start: 0.6941 (pp20) cc_final: 0.6716 (pm20) REVERT: D 825 MET cc_start: 0.3173 (OUTLIER) cc_final: 0.2515 (tpp) REVERT: E 90 GLU cc_start: 0.0793 (OUTLIER) cc_final: -0.0477 (pm20) REVERT: G 90 GLU cc_start: 0.0843 (OUTLIER) cc_final: -0.0503 (pm20) outliers start: 11 outliers final: 7 residues processed: 167 average time/residue: 1.1218 time to fit residues: 203.4815 Evaluate side-chains 168 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 158 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 825 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 0.0170 chunk 103 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS G 132 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.180233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.132265 restraints weight = 35761.196| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 3.47 r_work: 0.3044 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10712 Z= 0.129 Angle : 0.405 6.087 14506 Z= 0.228 Chirality : 0.035 0.109 1638 Planarity : 0.003 0.039 1766 Dihedral : 3.559 15.349 1434 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.55 % Allowed : 19.93 % Favored : 79.52 % 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: 4.15 (0.23), residues: 1308 helix: 3.88 (0.16), residues: 934 sheet: 0.65 (0.85), residues: 40 loop : -0.59 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 178 HIS 0.004 0.001 HIS E 205 PHE 0.016 0.001 PHE C 546 TYR 0.012 0.001 TYR B 523 ARG 0.002 0.000 ARG G 209 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3902.99 seconds wall clock time: 69 minutes 18.01 seconds (4158.01 seconds total)