Starting phenix.real_space_refine on Sun Nov 17 03:11:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ott_17184/11_2024/8ott_17184.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ott_17184/11_2024/8ott_17184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ott_17184/11_2024/8ott_17184.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ott_17184/11_2024/8ott_17184.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ott_17184/11_2024/8ott_17184.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ott_17184/11_2024/8ott_17184.cif" } resolution = 3.3 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= 0.002 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 14 5.16 5 C 7231 2.51 5 N 2441 2.21 5 O 2999 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12973 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 774 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 838 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 832 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2935 Classifications: {'DNA': 144} Link IDs: {'rna3p': 143} Chain: "J" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2969 Classifications: {'DNA': 144} Link IDs: {'rna3p': 143} Chain: "M" Number of atoms: 538 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 53, 269 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 2, 'TRANS': 50} Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 105 Conformer: "B" Number of residues, atoms: 53, 269 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 2, 'TRANS': 50} Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 105 Chain: "N" Number of atoms: 512 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 51, 256 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 1, 'TRANS': 49} Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 4, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 112 Conformer: "B" Number of residues, atoms: 51, 256 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 1, 'TRANS': 49} Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 4, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 112 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PTD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PTD:plan-2': 2, 'PTD:plan-1': 2} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-2': 1, 'PTD:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PTD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PTD:plan-2': 2, 'PTD:plan-1': 2} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PTD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PTD:plan-2': 2, 'PTD:plan-1': 2} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-2': 1, 'PTD:plan-1': 1} Unresolved non-hydrogen planarities: 2 Residues with excluded nonbonded symmetry interactions: 104 residue: pdb=" N AASN M 353 " occ=0.50 ... (8 atoms not shown) pdb=" CB BASN M 353 " occ=0.50 residue: pdb=" N AVAL M 354 " occ=0.50 ... (8 atoms not shown) pdb=" CB BVAL M 354 " occ=0.50 residue: pdb=" N ALYS M 355 " occ=0.50 ... (8 atoms not shown) pdb=" CB BLYS M 355 " occ=0.50 residue: pdb=" N AARG M 356 " occ=0.50 ... (8 atoms not shown) pdb=" CB BARG M 356 " occ=0.50 residue: pdb=" N AARG M 357 " occ=0.50 ... (8 atoms not shown) pdb=" CB BARG M 357 " occ=0.50 residue: pdb=" N ATHR M 358 " occ=0.50 ... (8 atoms not shown) pdb=" CB BTHR M 358 " occ=0.50 residue: pdb=" N AHIS M 359 " occ=0.50 ... (8 atoms not shown) pdb=" CB BHIS M 359 " occ=0.50 residue: pdb=" N AASN M 360 " occ=0.50 ... (8 atoms not shown) pdb=" CB BASN M 360 " occ=0.50 residue: pdb=" N AVAL M 361 " occ=0.50 ... (8 atoms not shown) pdb=" CB BVAL M 361 " occ=0.50 residue: pdb=" N ALEU M 362 " occ=0.50 ... (8 atoms not shown) pdb=" CB BLEU M 362 " occ=0.50 residue: pdb=" N AGLU M 363 " occ=0.50 ... (8 atoms not shown) pdb=" CB BGLU M 363 " occ=0.50 residue: pdb=" N AARG M 364 " occ=0.50 ... (8 atoms not shown) pdb=" CB BARG M 364 " occ=0.50 ... (remaining 92 not shown) Time building chain proxies: 7.94, per 1000 atoms: 0.61 Number of scatterers: 12973 At special positions: 0 Unit cell: (138.58, 114.92, 109.005, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 288 15.00 O 2999 8.00 N 2441 7.00 C 7231 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 1.1 seconds 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1816 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 10 sheets defined 76.1% alpha, 2.3% beta 143 base pairs and 274 stacking pairs defined. Time for finding SS restraints: 6.61 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.751A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.742A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.526A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.507A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.419A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.538A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.517A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 37 through 39 No H-bonds generated for 'chain 'G' and resid 37 through 39' Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.560A pdb=" N ALA H 107 " --> pdb=" O PRO H 103 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 354 through 381 removed outlier: 3.657A pdb=" N BILE M 381 " --> pdb=" O BLEU M 377 " (cutoff:3.500A) Processing helix chain 'M' and resid 382 through 385 Processing helix chain 'M' and resid 391 through 405 Processing helix chain 'N' and resid 24 through 50 Processing helix chain 'N' and resid 51 through 54 Processing helix chain 'N' and resid 59 through 73 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.989A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.987A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.678A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.832A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.872A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 550 hydrogen bonds defined for protein. 1608 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 370 hydrogen bonds 740 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 274 stacking parallelities Total time for adding SS restraints: 5.22 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2293 1.33 - 1.45: 4570 1.45 - 1.57: 6300 1.57 - 1.69: 574 1.69 - 1.81: 24 Bond restraints: 13761 Sorted by residual: bond pdb=" C3' DG J 101 " pdb=" C2' DG J 101 " ideal model delta sigma weight residual 1.525 1.560 -0.035 2.00e-02 2.50e+03 3.03e+00 bond pdb=" C3' DG I 99 " pdb=" C2' DG I 99 " ideal model delta sigma weight residual 1.525 1.558 -0.033 2.00e-02 2.50e+03 2.72e+00 bond pdb=" C3' DG I 40 " pdb=" C2' DG I 40 " ideal model delta sigma weight residual 1.525 1.558 -0.033 2.00e-02 2.50e+03 2.65e+00 bond pdb=" C1 PTD D 201 " pdb=" C2 PTD D 201 " ideal model delta sigma weight residual 1.499 1.531 -0.032 2.00e-02 2.50e+03 2.53e+00 bond pdb=" C1 PTD D 202 " pdb=" C2 PTD D 202 " ideal model delta sigma weight residual 1.499 1.531 -0.032 2.00e-02 2.50e+03 2.50e+00 ... (remaining 13756 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 17486 1.16 - 2.32: 1969 2.32 - 3.49: 364 3.49 - 4.65: 30 4.65 - 5.81: 2 Bond angle restraints: 19851 Sorted by residual: angle pdb=" C2' DG I 99 " pdb=" C1' DG I 99 " pdb=" N9 DG I 99 " ideal model delta sigma weight residual 113.50 118.08 -4.58 1.50e+00 4.44e-01 9.31e+00 angle pdb=" O4' DG I 67 " pdb=" C1' DG I 67 " pdb=" N9 DG I 67 " ideal model delta sigma weight residual 108.40 104.32 4.08 1.50e+00 4.44e-01 7.40e+00 angle pdb=" C ARG G 32 " pdb=" CA ARG G 32 " pdb=" CB ARG G 32 " ideal model delta sigma weight residual 110.81 106.48 4.33 1.60e+00 3.91e-01 7.32e+00 angle pdb=" CG ARG B 92 " pdb=" CD ARG B 92 " pdb=" NE ARG B 92 " ideal model delta sigma weight residual 112.00 106.19 5.81 2.20e+00 2.07e-01 6.98e+00 angle pdb=" C2' DC I 70 " pdb=" C1' DC I 70 " pdb=" N1 DC I 70 " ideal model delta sigma weight residual 113.50 117.42 -3.92 1.50e+00 4.44e-01 6.82e+00 ... (remaining 19846 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.68: 6255 31.68 - 63.37: 1249 63.37 - 95.05: 8 95.05 - 126.73: 0 126.73 - 158.41: 1 Dihedral angle restraints: 7513 sinusoidal: 4716 harmonic: 2797 Sorted by residual: dihedral pdb=" CA ALA G 14 " pdb=" C ALA G 14 " pdb=" N LYS G 15 " pdb=" CA LYS G 15 " ideal model delta harmonic sigma weight residual -180.00 -150.75 -29.25 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" C4' DT I 77 " pdb=" C3' DT I 77 " pdb=" O3' DT I 77 " pdb=" P DC I 78 " ideal model delta sinusoidal sigma weight residual 220.00 61.59 158.41 1 3.50e+01 8.16e-04 1.51e+01 dihedral pdb=" CA TYR D 83 " pdb=" C TYR D 83 " pdb=" N ASN D 84 " pdb=" CA ASN D 84 " ideal model delta harmonic sigma weight residual 180.00 160.95 19.05 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 7510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1728 0.045 - 0.089: 414 0.089 - 0.134: 108 0.134 - 0.179: 41 0.179 - 0.223: 4 Chirality restraints: 2295 Sorted by residual: chirality pdb=" CA LYS G 15 " pdb=" N LYS G 15 " pdb=" C LYS G 15 " pdb=" CB LYS G 15 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA LYS F 77 " pdb=" N LYS F 77 " pdb=" C LYS F 77 " pdb=" CB LYS F 77 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" C4' DG I 67 " pdb=" C5' DG I 67 " pdb=" O4' DG I 67 " pdb=" C3' DG I 67 " both_signs ideal model delta sigma weight residual False -2.53 -2.34 -0.19 2.00e-01 2.50e+01 8.98e-01 ... (remaining 2292 not shown) Planarity restraints: 1541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 67 " 0.064 2.00e-02 2.50e+03 2.56e-02 1.96e+01 pdb=" N9 DG I 67 " -0.052 2.00e-02 2.50e+03 pdb=" C8 DG I 67 " -0.010 2.00e-02 2.50e+03 pdb=" N7 DG I 67 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DG I 67 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DG I 67 " 0.013 2.00e-02 2.50e+03 pdb=" O6 DG I 67 " 0.021 2.00e-02 2.50e+03 pdb=" N1 DG I 67 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DG I 67 " -0.003 2.00e-02 2.50e+03 pdb=" N2 DG I 67 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DG I 67 " -0.010 2.00e-02 2.50e+03 pdb=" C4 DG I 67 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 92 " 0.378 9.50e-02 1.11e+02 1.69e-01 1.77e+01 pdb=" NE ARG B 92 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG B 92 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 92 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 92 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 69 " 0.052 2.00e-02 2.50e+03 2.19e-02 1.31e+01 pdb=" N9 DA I 69 " -0.043 2.00e-02 2.50e+03 pdb=" C8 DA I 69 " -0.006 2.00e-02 2.50e+03 pdb=" N7 DA I 69 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DA I 69 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DA I 69 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 69 " 0.022 2.00e-02 2.50e+03 pdb=" N1 DA I 69 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 69 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA I 69 " -0.009 2.00e-02 2.50e+03 pdb=" C4 DA I 69 " -0.009 2.00e-02 2.50e+03 ... (remaining 1538 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 5905 2.99 - 3.47: 12237 3.47 - 3.95: 25579 3.95 - 4.42: 28008 4.42 - 4.90: 37126 Nonbonded interactions: 108855 Sorted by model distance: nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.513 3.040 nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.520 3.040 nonbonded pdb=" N6 DA I 69 " pdb=" O6 DG J 78 " model vdw 2.528 3.120 nonbonded pdb=" O LEU A 103 " pdb=" OG1 THR A 107 " model vdw 2.556 3.040 nonbonded pdb=" N GLN G 24 " pdb=" OE1 GLU G 56 " model vdw 2.559 3.120 ... (remaining 108850 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' selection = (chain 'E' and (resid 40 through 133 or resid 201 through 202)) } ncs_group { reference = (chain 'B' and resid 22 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 10 through 115 or (resid 116 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain 'G' and resid 10 through 116) } ncs_group { reference = (chain 'D' and (resid 32 through 124 or resid 201)) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.95 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 35.140 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13761 Z= 0.272 Angle : 0.774 5.811 19851 Z= 0.478 Chirality : 0.046 0.223 2295 Planarity : 0.010 0.169 1541 Dihedral : 24.297 158.413 5697 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.16 % Allowed : 0.79 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.24), residues: 939 helix: 0.97 (0.17), residues: 703 sheet: None (None), residues: 0 loop : 0.12 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS D 49 PHE 0.023 0.003 PHE H 70 TYR 0.020 0.003 TYR C 57 ARG 0.006 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 34 LYS cc_start: 0.8808 (tptm) cc_final: 0.8485 (tppt) outliers start: 1 outliers final: 1 residues processed: 190 average time/residue: 0.4192 time to fit residues: 101.4865 Evaluate side-chains 116 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 30.0000 chunk 33 optimal weight: 0.0670 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN D 49 HIS F 75 HIS H 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 13761 Z= 0.206 Angle : 0.585 7.124 19851 Z= 0.346 Chirality : 0.035 0.160 2295 Planarity : 0.004 0.039 1541 Dihedral : 28.576 156.862 4203 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.11 % Allowed : 10.16 % Favored : 88.73 % 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: 3.31 (0.27), residues: 939 helix: 2.82 (0.19), residues: 711 sheet: None (None), residues: 0 loop : 0.11 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 49 PHE 0.009 0.001 PHE A 67 TYR 0.013 0.002 TYR D 40 ARG 0.007 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 142 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: D 34 LYS cc_start: 0.8947 (tptm) cc_final: 0.8568 (tppt) REVERT: E 77 ASP cc_start: 0.6402 (m-30) cc_final: 0.6131 (m-30) REVERT: F 74 GLU cc_start: 0.6927 (tp30) cc_final: 0.6638 (tp30) REVERT: G 73 ASN cc_start: 0.8684 (m-40) cc_final: 0.8391 (t0) REVERT: H 59 MET cc_start: 0.8538 (tpt) cc_final: 0.8277 (mmm) outliers start: 7 outliers final: 4 residues processed: 145 average time/residue: 0.2965 time to fit residues: 58.8431 Evaluate side-chains 114 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 110 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.0670 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 0.0070 chunk 100 optimal weight: 40.0000 chunk 108 optimal weight: 50.0000 chunk 89 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 overall best weight: 2.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 112 GLN H 67 ASN H 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13761 Z= 0.290 Angle : 0.598 9.680 19851 Z= 0.350 Chirality : 0.036 0.158 2295 Planarity : 0.004 0.031 1541 Dihedral : 29.220 159.809 4203 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.43 % Allowed : 12.70 % Favored : 85.87 % 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: 3.61 (0.27), residues: 939 helix: 3.09 (0.18), residues: 711 sheet: None (None), residues: 0 loop : 0.01 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.010 0.001 PHE A 67 TYR 0.020 0.002 TYR H 121 ARG 0.006 0.001 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: C 110 ASN cc_start: 0.8166 (m-40) cc_final: 0.7797 (m110) REVERT: D 34 LYS cc_start: 0.9045 (tptm) cc_final: 0.8724 (tppt) REVERT: E 77 ASP cc_start: 0.6707 (m-30) cc_final: 0.6462 (m-30) REVERT: F 52 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6765 (mm-30) REVERT: G 13 LYS cc_start: 0.7739 (tptt) cc_final: 0.7367 (tppt) REVERT: G 38 ASN cc_start: 0.8058 (m110) cc_final: 0.7807 (m-40) REVERT: H 59 MET cc_start: 0.8694 (tpt) cc_final: 0.8286 (tpt) outliers start: 9 outliers final: 4 residues processed: 128 average time/residue: 0.3005 time to fit residues: 52.6066 Evaluate side-chains 112 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 67 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 50.0000 chunk 52 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13761 Z= 0.198 Angle : 0.538 6.792 19851 Z= 0.321 Chirality : 0.033 0.148 2295 Planarity : 0.004 0.035 1541 Dihedral : 28.703 158.086 4203 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.59 % Allowed : 13.17 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.96 (0.27), residues: 939 helix: 3.39 (0.18), residues: 711 sheet: None (None), residues: 0 loop : -0.02 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 109 PHE 0.009 0.001 PHE E 67 TYR 0.015 0.001 TYR H 40 ARG 0.005 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: C 110 ASN cc_start: 0.8134 (m-40) cc_final: 0.7864 (m110) REVERT: D 34 LYS cc_start: 0.9130 (tptm) cc_final: 0.8795 (tppt) REVERT: F 52 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6854 (mm-30) REVERT: H 59 MET cc_start: 0.8617 (tpt) cc_final: 0.8232 (tpt) outliers start: 10 outliers final: 5 residues processed: 123 average time/residue: 0.2718 time to fit residues: 47.4666 Evaluate side-chains 113 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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: 0.8433 moved from start: 0.4940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13761 Z= 0.249 Angle : 0.570 7.695 19851 Z= 0.335 Chirality : 0.035 0.150 2295 Planarity : 0.004 0.035 1541 Dihedral : 29.005 159.202 4199 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.27 % Allowed : 13.33 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.98 (0.27), residues: 939 helix: 3.43 (0.18), residues: 711 sheet: None (None), residues: 0 loop : -0.15 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 109 PHE 0.010 0.001 PHE A 67 TYR 0.016 0.001 TYR H 40 ARG 0.007 0.000 ARG D 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: D 34 LYS cc_start: 0.9122 (tptm) cc_final: 0.8854 (tppt) REVERT: F 52 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6998 (mm-30) REVERT: F 74 GLU cc_start: 0.6941 (tp30) cc_final: 0.6604 (tp30) REVERT: H 59 MET cc_start: 0.8640 (tpt) cc_final: 0.8271 (tpt) outliers start: 8 outliers final: 4 residues processed: 121 average time/residue: 0.2663 time to fit residues: 46.3184 Evaluate side-chains 113 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 109 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.8385 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13761 Z= 0.189 Angle : 0.597 19.000 19851 Z= 0.343 Chirality : 0.033 0.293 2295 Planarity : 0.004 0.036 1541 Dihedral : 28.663 157.652 4199 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.63 % Allowed : 13.81 % Favored : 85.56 % 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 (0.27), residues: 939 helix: 3.46 (0.18), residues: 714 sheet: None (None), residues: 0 loop : -0.14 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 109 PHE 0.009 0.001 PHE E 67 TYR 0.013 0.001 TYR H 40 ARG 0.008 0.000 ARG D 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: D 34 LYS cc_start: 0.9129 (tptm) cc_final: 0.8875 (tppt) REVERT: H 59 MET cc_start: 0.8591 (tpt) cc_final: 0.8219 (tpt) outliers start: 4 outliers final: 2 residues processed: 120 average time/residue: 0.2359 time to fit residues: 42.0966 Evaluate side-chains 109 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 107 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 100 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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: 0.8461 moved from start: 0.5353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 13761 Z= 0.301 Angle : 0.648 20.043 19851 Z= 0.369 Chirality : 0.037 0.370 2295 Planarity : 0.004 0.034 1541 Dihedral : 29.187 157.980 4199 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.48 % Allowed : 16.19 % Favored : 83.33 % 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: 3.97 (0.27), residues: 939 helix: 3.55 (0.18), residues: 702 sheet: None (None), residues: 0 loop : -0.47 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.002 HIS H 109 PHE 0.010 0.001 PHE A 67 TYR 0.014 0.002 TYR D 83 ARG 0.007 0.000 ARG D 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 111 time to evaluate : 0.994 Fit side-chains REVERT: A 76 GLN cc_start: 0.8827 (tm-30) cc_final: 0.8585 (pp30) REVERT: D 34 LYS cc_start: 0.9100 (tptm) cc_final: 0.8828 (tppt) outliers start: 3 outliers final: 2 residues processed: 113 average time/residue: 0.2649 time to fit residues: 43.0887 Evaluate side-chains 108 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 100 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 0.0770 chunk 67 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS H 109 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13761 Z= 0.280 Angle : 0.645 20.285 19851 Z= 0.368 Chirality : 0.037 0.413 2295 Planarity : 0.004 0.035 1541 Dihedral : 29.152 157.163 4199 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.48 % Allowed : 16.51 % Favored : 83.02 % Cbeta Deviations : 0.11 % 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: 3.91 (0.27), residues: 939 helix: 3.52 (0.18), residues: 702 sheet: None (None), residues: 0 loop : -0.53 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS H 109 PHE 0.010 0.001 PHE A 67 TYR 0.017 0.001 TYR H 40 ARG 0.010 0.000 ARG D 33 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 108 time to evaluate : 0.983 Fit side-chains REVERT: A 76 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8596 (pp30) REVERT: D 34 LYS cc_start: 0.9045 (tptm) cc_final: 0.8792 (tppt) REVERT: G 91 GLU cc_start: 0.7559 (pm20) cc_final: 0.7177 (pm20) outliers start: 3 outliers final: 2 residues processed: 110 average time/residue: 0.2623 time to fit residues: 41.7180 Evaluate side-chains 102 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 100 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.5680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13761 Z= 0.261 Angle : 0.664 21.478 19851 Z= 0.376 Chirality : 0.037 0.433 2295 Planarity : 0.004 0.036 1541 Dihedral : 29.125 156.734 4199 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.79 % Allowed : 16.83 % Favored : 82.38 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 3.92 (0.27), residues: 939 helix: 3.53 (0.18), residues: 705 sheet: None (None), residues: 0 loop : -0.60 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 109 PHE 0.010 0.001 PHE E 67 TYR 0.016 0.001 TYR H 40 ARG 0.010 0.000 ARG D 33 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8624 (pp30) REVERT: D 34 LYS cc_start: 0.8991 (tptm) cc_final: 0.8751 (tppt) REVERT: G 91 GLU cc_start: 0.7524 (pm20) cc_final: 0.7200 (pm20) outliers start: 5 outliers final: 3 residues processed: 111 average time/residue: 0.2490 time to fit residues: 40.2354 Evaluate side-chains 106 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 103 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 109 optimal weight: 50.0000 chunk 100 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 9 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.5791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13761 Z= 0.260 Angle : 0.681 18.933 19851 Z= 0.384 Chirality : 0.037 0.417 2295 Planarity : 0.004 0.069 1541 Dihedral : 29.129 156.218 4199 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.79 % Allowed : 16.98 % Favored : 82.22 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 3.94 (0.27), residues: 939 helix: 3.58 (0.18), residues: 702 sheet: None (None), residues: 0 loop : -0.66 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.010 0.001 PHE E 67 TYR 0.016 0.001 TYR H 40 ARG 0.010 0.000 ARG B 23 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8857 (tm-30) cc_final: 0.8636 (pp30) REVERT: B 93 GLN cc_start: 0.8403 (mt0) cc_final: 0.8160 (tt0) REVERT: D 34 LYS cc_start: 0.8956 (tptm) cc_final: 0.8740 (tppt) REVERT: G 91 GLU cc_start: 0.7486 (pm20) cc_final: 0.7153 (pm20) outliers start: 5 outliers final: 3 residues processed: 112 average time/residue: 0.2353 time to fit residues: 39.0446 Evaluate side-chains 105 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 102 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 87 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.086000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.062335 restraints weight = 56430.598| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.90 r_work: 0.3051 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.5898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 13761 Z= 0.233 Angle : 0.684 18.666 19851 Z= 0.383 Chirality : 0.037 0.479 2295 Planarity : 0.004 0.072 1541 Dihedral : 28.945 154.991 4199 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.48 % Allowed : 17.46 % Favored : 82.06 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: 3.94 (0.27), residues: 939 helix: 3.55 (0.18), residues: 706 sheet: None (None), residues: 0 loop : -0.61 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS D 109 PHE 0.010 0.001 PHE E 67 TYR 0.015 0.001 TYR G 57 ARG 0.009 0.000 ARG B 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2499.37 seconds wall clock time: 46 minutes 9.41 seconds (2769.41 seconds total)