Starting phenix.real_space_refine on Sun Dec 10 18:50:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg4_31105/12_2023/7eg4_31105_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg4_31105/12_2023/7eg4_31105.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg4_31105/12_2023/7eg4_31105.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg4_31105/12_2023/7eg4_31105.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg4_31105/12_2023/7eg4_31105_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg4_31105/12_2023/7eg4_31105_trim_updated.pdb" } resolution = 3.2 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 Mg 4 5.21 5 S 98 5.16 5 C 9770 2.51 5 N 2582 2.21 5 O 2802 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 675": "OE1" <-> "OE2" Residue "C GLU 687": "OE1" <-> "OE2" Residue "C GLU 701": "OE1" <-> "OE2" Residue "C ARG 705": "NH1" <-> "NH2" Residue "C ARG 709": "NH1" <-> "NH2" Residue "C ARG 717": "NH1" <-> "NH2" Residue "C GLU 726": "OE1" <-> "OE2" Residue "C ARG 733": "NH1" <-> "NH2" Residue "C GLU 734": "OE1" <-> "OE2" Residue "C GLU 743": "OE1" <-> "OE2" Residue "C GLU 935": "OE1" <-> "OE2" Residue "C ARG 938": "NH1" <-> "NH2" Residue "D ARG 20": "NH1" <-> "NH2" Residue "D ARG 28": "NH1" <-> "NH2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D ARG 46": "NH1" <-> "NH2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "D GLU 92": "OE1" <-> "OE2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 129": "NH1" <-> "NH2" Residue "D ARG 166": "NH1" <-> "NH2" Residue "D ARG 187": "NH1" <-> "NH2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "D ARG 217": "NH1" <-> "NH2" Residue "D PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 253": "OE1" <-> "OE2" Residue "D GLU 261": "OE1" <-> "OE2" Residue "D ARG 262": "NH1" <-> "NH2" Residue "D GLU 263": "OE1" <-> "OE2" Residue "D GLU 265": "OE1" <-> "OE2" Residue "D ARG 269": "NH1" <-> "NH2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D GLU 308": "OE1" <-> "OE2" Residue "D GLU 318": "OE1" <-> "OE2" Residue "D ARG 328": "NH1" <-> "NH2" Residue "D ARG 334": "NH1" <-> "NH2" Residue "D GLU 353": "OE1" <-> "OE2" Residue "D ARG 378": "NH1" <-> "NH2" Residue "D GLU 412": "OE1" <-> "OE2" Residue "D ARG 426": "NH1" <-> "NH2" Residue "D GLU 464": "OE1" <-> "OE2" Residue "D GLU 465": "OE1" <-> "OE2" Residue "D GLU 520": "OE1" <-> "OE2" Residue "D ARG 527": "NH1" <-> "NH2" Residue "A GLU 675": "OE1" <-> "OE2" Residue "A GLU 687": "OE1" <-> "OE2" Residue "A GLU 701": "OE1" <-> "OE2" Residue "A ARG 705": "NH1" <-> "NH2" Residue "A ARG 709": "NH1" <-> "NH2" Residue "A ARG 717": "NH1" <-> "NH2" Residue "A GLU 726": "OE1" <-> "OE2" Residue "A ARG 733": "NH1" <-> "NH2" Residue "A GLU 734": "OE1" <-> "OE2" Residue "A GLU 743": "OE1" <-> "OE2" Residue "A GLU 935": "OE1" <-> "OE2" Residue "A ARG 938": "NH1" <-> "NH2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B ARG 37": "NH1" <-> "NH2" Residue "B GLU 42": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 166": "NH1" <-> "NH2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "B ARG 217": "NH1" <-> "NH2" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 253": "OE1" <-> "OE2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "B ARG 262": "NH1" <-> "NH2" Residue "B GLU 263": "OE1" <-> "OE2" Residue "B GLU 265": "OE1" <-> "OE2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B ARG 306": "NH1" <-> "NH2" Residue "B GLU 308": "OE1" <-> "OE2" Residue "B GLU 318": "OE1" <-> "OE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 334": "NH1" <-> "NH2" Residue "B GLU 353": "OE1" <-> "OE2" Residue "B ARG 378": "NH1" <-> "NH2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "B ARG 426": "NH1" <-> "NH2" Residue "B GLU 464": "OE1" <-> "OE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B GLU 520": "OE1" <-> "OE2" Residue "B ARG 527": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 15258 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 3004 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 18, 'TRANS': 353} Chain breaks: 2 Chain: "D" Number of atoms: 4600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4600 Classifications: {'peptide': 567} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 550} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 3004 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 18, 'TRANS': 353} Chain breaks: 2 Chain: "B" Number of atoms: 4600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4600 Classifications: {'peptide': 567} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 550} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 24 Unusual residues: {' MG': 2, 'J36': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 24 Unusual residues: {' MG': 2, 'J36': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5222 SG CYS D 277 24.703 60.259 74.608 1.00 63.56 S ATOM 5495 SG CYS D 311 25.288 59.169 77.864 1.00 50.53 S ATOM 5501 SG CYS D 312 28.122 61.185 76.154 1.00 45.94 S ATOM 12826 SG CYS B 277 74.874 74.149 74.614 1.00 63.56 S ATOM 13099 SG CYS B 311 74.289 75.238 77.871 1.00 50.53 S ATOM 13105 SG CYS B 312 71.455 73.223 76.160 1.00 45.94 S Time building chain proxies: 8.25, per 1000 atoms: 0.54 Number of scatterers: 15258 At special positions: 0 Unit cell: (100.672, 135.312, 128.817, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 98 16.00 Mg 4 11.99 O 2802 8.00 N 2582 7.00 C 9770 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS D 381 " - pdb=" SG CYS D 411 " distance=2.03 Simple disulfide: pdb=" SG CYS B 381 " - pdb=" SG CYS B 411 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.24 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" ND1 HIS B 275 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 312 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 277 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 311 " pdb=" ZN D 601 " pdb="ZN ZN D 601 " - pdb=" ND1 HIS D 275 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 312 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 277 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 311 " Number of angles added : 6 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3568 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 8 sheets defined 41.9% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.06 Creating SS restraints... Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 696 through 702 Processing helix chain 'C' and resid 710 through 722 Processing helix chain 'C' and resid 724 through 727 No H-bonds generated for 'chain 'C' and resid 724 through 727' Processing helix chain 'C' and resid 732 through 745 Processing helix chain 'C' and resid 754 through 768 Processing helix chain 'C' and resid 817 through 820 No H-bonds generated for 'chain 'C' and resid 817 through 820' Processing helix chain 'C' and resid 823 through 834 Processing helix chain 'C' and resid 845 through 850 Processing helix chain 'C' and resid 854 through 857 No H-bonds generated for 'chain 'C' and resid 854 through 857' Processing helix chain 'C' and resid 864 through 879 Processing helix chain 'C' and resid 891 through 908 removed outlier: 3.837A pdb=" N THR C 908 " --> pdb=" O ALA C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 924 removed outlier: 4.957A pdb=" N PHE C 914 " --> pdb=" O LYS C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 935 through 950 Processing helix chain 'C' and resid 953 through 955 No H-bonds generated for 'chain 'C' and resid 953 through 955' Processing helix chain 'C' and resid 958 through 980 Processing helix chain 'C' and resid 997 through 1007 Processing helix chain 'C' and resid 1009 through 1018 Processing helix chain 'C' and resid 1074 through 1101 Processing helix chain 'D' and resid 25 through 30 Processing helix chain 'D' and resid 34 through 53 Processing helix chain 'D' and resid 78 through 86 Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 174 through 186 Processing helix chain 'D' and resid 215 through 231 Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 257 through 269 Processing helix chain 'D' and resid 334 through 342 Processing helix chain 'D' and resid 351 through 358 Processing helix chain 'D' and resid 395 through 401 Processing helix chain 'D' and resid 404 through 413 removed outlier: 4.312A pdb=" N GLN D 408 " --> pdb=" O GLU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 431 No H-bonds generated for 'chain 'D' and resid 428 through 431' Processing helix chain 'D' and resid 467 through 483 Processing helix chain 'D' and resid 512 through 514 No H-bonds generated for 'chain 'D' and resid 512 through 514' Processing helix chain 'D' and resid 520 through 523 removed outlier: 3.915A pdb=" N TYR D 523 " --> pdb=" O GLU D 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 520 through 523' Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 553 through 558 removed outlier: 3.629A pdb=" N ILE D 557 " --> pdb=" O ASN D 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 689 No H-bonds generated for 'chain 'A' and resid 687 through 689' Processing helix chain 'A' and resid 696 through 702 Processing helix chain 'A' and resid 710 through 722 Processing helix chain 'A' and resid 724 through 727 No H-bonds generated for 'chain 'A' and resid 724 through 727' Processing helix chain 'A' and resid 732 through 745 Processing helix chain 'A' and resid 754 through 768 Processing helix chain 'A' and resid 817 through 820 No H-bonds generated for 'chain 'A' and resid 817 through 820' Processing helix chain 'A' and resid 823 through 834 Processing helix chain 'A' and resid 845 through 850 Processing helix chain 'A' and resid 854 through 857 No H-bonds generated for 'chain 'A' and resid 854 through 857' Processing helix chain 'A' and resid 864 through 879 Processing helix chain 'A' and resid 891 through 908 removed outlier: 3.837A pdb=" N THR A 908 " --> pdb=" O ALA A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 924 removed outlier: 4.958A pdb=" N PHE A 914 " --> pdb=" O LYS A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 950 Processing helix chain 'A' and resid 953 through 955 No H-bonds generated for 'chain 'A' and resid 953 through 955' Processing helix chain 'A' and resid 958 through 980 Processing helix chain 'A' and resid 997 through 1007 Processing helix chain 'A' and resid 1009 through 1018 Processing helix chain 'A' and resid 1074 through 1101 Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 34 through 53 Processing helix chain 'B' and resid 78 through 86 Processing helix chain 'B' and resid 139 through 151 Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 215 through 231 Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 257 through 269 Processing helix chain 'B' and resid 334 through 342 Processing helix chain 'B' and resid 351 through 358 Processing helix chain 'B' and resid 395 through 401 Processing helix chain 'B' and resid 404 through 413 removed outlier: 4.312A pdb=" N GLN B 408 " --> pdb=" O GLU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 431 No H-bonds generated for 'chain 'B' and resid 428 through 431' Processing helix chain 'B' and resid 467 through 483 Processing helix chain 'B' and resid 512 through 514 No H-bonds generated for 'chain 'B' and resid 512 through 514' Processing helix chain 'B' and resid 520 through 523 removed outlier: 3.914A pdb=" N TYR B 523 " --> pdb=" O GLU B 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 520 through 523' Processing helix chain 'B' and resid 529 through 540 Processing helix chain 'B' and resid 553 through 558 removed outlier: 3.629A pdb=" N ILE B 557 " --> pdb=" O ASN B 553 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'D' and resid 15 through 17 removed outlier: 6.520A pdb=" N VAL D 58 " --> pdb=" O LEU D 16 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 127 through 129 Processing sheet with id= C, first strand: chain 'D' and resid 204 through 207 removed outlier: 6.534A pdb=" N TYR D 236 " --> pdb=" O GLU D 205 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N LYS D 207 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE D 238 " --> pdb=" O LYS D 207 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 440 through 443 removed outlier: 7.042A pdb=" N PHE D 458 " --> pdb=" O LEU D 441 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 15 through 17 removed outlier: 6.521A pdb=" N VAL B 58 " --> pdb=" O LEU B 16 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 127 through 129 Processing sheet with id= G, first strand: chain 'B' and resid 204 through 207 removed outlier: 6.534A pdb=" N TYR B 236 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N LYS B 207 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE B 238 " --> pdb=" O LYS B 207 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 440 through 443 removed outlier: 7.043A pdb=" N PHE B 458 " --> pdb=" O LEU B 441 " (cutoff:3.500A) 542 hydrogen bonds defined for protein. 1548 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.21 Time building geometry restraints manager: 6.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4903 1.34 - 1.46: 2841 1.46 - 1.57: 7704 1.57 - 1.69: 0 1.69 - 1.81: 150 Bond restraints: 15598 Sorted by residual: bond pdb=" N GLU D 345 " pdb=" CA GLU D 345 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.56e-02 4.11e+03 7.45e+00 bond pdb=" N GLU B 345 " pdb=" CA GLU B 345 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.56e-02 4.11e+03 7.45e+00 bond pdb=" C GLU B 393 " pdb=" N ASN B 394 " ideal model delta sigma weight residual 1.332 1.301 0.031 1.40e-02 5.10e+03 4.93e+00 bond pdb=" C GLU D 393 " pdb=" N ASN D 394 " ideal model delta sigma weight residual 1.332 1.301 0.031 1.40e-02 5.10e+03 4.93e+00 bond pdb=" C10 J36 C1201 " pdb=" C8 J36 C1201 " ideal model delta sigma weight residual 1.418 1.461 -0.043 2.00e-02 2.50e+03 4.62e+00 ... (remaining 15593 not shown) Histogram of bond angle deviations from ideal: 98.94 - 106.08: 295 106.08 - 113.22: 8545 113.22 - 120.37: 6183 120.37 - 127.51: 5881 127.51 - 134.65: 160 Bond angle restraints: 21064 Sorted by residual: angle pdb=" C PRO B 502 " pdb=" N GLU B 503 " pdb=" CA GLU B 503 " ideal model delta sigma weight residual 122.35 128.23 -5.88 1.46e+00 4.69e-01 1.62e+01 angle pdb=" C PRO D 502 " pdb=" N GLU D 503 " pdb=" CA GLU D 503 " ideal model delta sigma weight residual 122.35 128.21 -5.86 1.46e+00 4.69e-01 1.61e+01 angle pdb=" N ASP B 546 " pdb=" CA ASP B 546 " pdb=" C ASP B 546 " ideal model delta sigma weight residual 114.56 110.28 4.28 1.27e+00 6.20e-01 1.14e+01 angle pdb=" N ASP D 546 " pdb=" CA ASP D 546 " pdb=" C ASP D 546 " ideal model delta sigma weight residual 114.56 110.31 4.25 1.27e+00 6.20e-01 1.12e+01 angle pdb=" C TYR C 807 " pdb=" N ASN C 808 " pdb=" CA ASN C 808 " ideal model delta sigma weight residual 121.54 127.91 -6.37 1.91e+00 2.74e-01 1.11e+01 ... (remaining 21059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 8466 17.99 - 35.97: 806 35.97 - 53.96: 120 53.96 - 71.95: 20 71.95 - 89.93: 16 Dihedral angle restraints: 9428 sinusoidal: 3912 harmonic: 5516 Sorted by residual: dihedral pdb=" CB CYS B 381 " pdb=" SG CYS B 381 " pdb=" SG CYS B 411 " pdb=" CB CYS B 411 " ideal model delta sinusoidal sigma weight residual 93.00 163.11 -70.11 1 1.00e+01 1.00e-02 6.33e+01 dihedral pdb=" CB CYS D 381 " pdb=" SG CYS D 381 " pdb=" SG CYS D 411 " pdb=" CB CYS D 411 " ideal model delta sinusoidal sigma weight residual 93.00 163.10 -70.10 1 1.00e+01 1.00e-02 6.33e+01 dihedral pdb=" CA TYR B 390 " pdb=" C TYR B 390 " pdb=" N THR B 391 " pdb=" CA THR B 391 " ideal model delta harmonic sigma weight residual -180.00 -152.50 -27.50 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 9425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1407 0.037 - 0.074: 667 0.074 - 0.111: 159 0.111 - 0.148: 43 0.148 - 0.185: 10 Chirality restraints: 2286 Sorted by residual: chirality pdb=" CA PRO D 382 " pdb=" N PRO D 382 " pdb=" C PRO D 382 " pdb=" CB PRO D 382 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.18 2.00e-01 2.50e+01 8.51e-01 chirality pdb=" CA PRO B 382 " pdb=" N PRO B 382 " pdb=" C PRO B 382 " pdb=" CB PRO B 382 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.40e-01 chirality pdb=" CA PHE D 550 " pdb=" N PHE D 550 " pdb=" C PHE D 550 " pdb=" CB PHE D 550 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.47e-01 ... (remaining 2283 not shown) Planarity restraints: 2694 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 344 " -0.021 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C ALA D 344 " 0.072 2.00e-02 2.50e+03 pdb=" O ALA D 344 " -0.027 2.00e-02 2.50e+03 pdb=" N GLU D 345 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C1087 " -0.021 2.00e-02 2.50e+03 4.15e-02 1.72e+01 pdb=" C LYS C1087 " 0.072 2.00e-02 2.50e+03 pdb=" O LYS C1087 " -0.027 2.00e-02 2.50e+03 pdb=" N LYS C1088 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A1087 " -0.021 2.00e-02 2.50e+03 4.15e-02 1.72e+01 pdb=" C LYS A1087 " 0.072 2.00e-02 2.50e+03 pdb=" O LYS A1087 " -0.027 2.00e-02 2.50e+03 pdb=" N LYS A1088 " -0.024 2.00e-02 2.50e+03 ... (remaining 2691 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 110 2.52 - 3.11: 12189 3.11 - 3.71: 22046 3.71 - 4.30: 32593 4.30 - 4.90: 55472 Nonbonded interactions: 122410 Sorted by model distance: nonbonded pdb=" OD2 ASP C 837 " pdb="MG MG C1202 " model vdw 1.920 2.170 nonbonded pdb=" OD2 ASP A 837 " pdb="MG MG A1202 " model vdw 1.921 2.170 nonbonded pdb=" OG1 THR B 152 " pdb=" O GLY B 154 " model vdw 2.101 2.440 nonbonded pdb=" OG1 THR D 152 " pdb=" O GLY D 154 " model vdw 2.101 2.440 nonbonded pdb=" NE2 HIS C 836 " pdb="MG MG C1202 " model vdw 2.111 2.250 ... (remaining 122405 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.470 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: 2.590 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 45.490 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.090 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 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 : 0.008 0.052 15598 Z= 0.542 Angle : 0.699 6.365 21064 Z= 0.400 Chirality : 0.045 0.185 2286 Planarity : 0.005 0.048 2694 Dihedral : 14.251 89.934 5854 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.89 % Favored : 87.11 % Rotamer: Outliers : 0.12 % Allowed : 5.50 % Favored : 94.38 % 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: -3.12 (0.17), residues: 1862 helix: -0.69 (0.16), residues: 854 sheet: -2.53 (0.35), residues: 166 loop : -3.54 (0.18), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 110 HIS 0.004 0.001 HIS D 380 PHE 0.030 0.002 PHE D 550 TYR 0.022 0.002 TYR D 70 ARG 0.007 0.001 ARG B 387 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 229 time to evaluate : 1.931 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 231 average time/residue: 0.3496 time to fit residues: 112.7766 Evaluate side-chains 148 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.732 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 48 optimal weight: 0.0980 chunk 95 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 108 optimal weight: 0.2980 chunk 168 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 713 GLN C 936 ASN C1081 GLN D 172 GLN D 284 ASN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN D 377 GLN D 509 GLN D 553 ASN A 713 GLN A 936 ASN A1081 GLN B 172 GLN B 216 GLN B 284 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 377 GLN B 509 GLN B 553 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15598 Z= 0.191 Angle : 0.554 10.271 21064 Z= 0.289 Chirality : 0.041 0.191 2286 Planarity : 0.004 0.051 2694 Dihedral : 4.485 26.368 2074 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 1.50 % Allowed : 9.51 % Favored : 89.00 % 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: -1.79 (0.19), residues: 1862 helix: 0.62 (0.17), residues: 870 sheet: -2.21 (0.35), residues: 184 loop : -3.09 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 110 HIS 0.002 0.001 HIS B 380 PHE 0.030 0.001 PHE D 550 TYR 0.028 0.001 TYR D 301 ARG 0.012 0.000 ARG B 387 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 169 time to evaluate : 1.727 Fit side-chains outliers start: 25 outliers final: 15 residues processed: 187 average time/residue: 0.2987 time to fit residues: 82.6220 Evaluate side-chains 163 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 148 time to evaluate : 1.798 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1677 time to fit residues: 6.9747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 140 optimal weight: 0.7980 chunk 115 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 169 optimal weight: 8.9990 chunk 182 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 167 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 135 optimal weight: 0.6980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN B 41 ASN B 284 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15598 Z= 0.316 Angle : 0.568 8.339 21064 Z= 0.299 Chirality : 0.043 0.190 2286 Planarity : 0.005 0.057 2694 Dihedral : 4.535 28.057 2074 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 1.56 % Allowed : 13.10 % Favored : 85.35 % 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: -1.28 (0.20), residues: 1862 helix: 1.05 (0.18), residues: 854 sheet: -1.83 (0.36), residues: 184 loop : -2.79 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 110 HIS 0.005 0.001 HIS B 323 PHE 0.029 0.001 PHE B 550 TYR 0.013 0.001 TYR A 738 ARG 0.009 0.000 ARG B 387 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 166 time to evaluate : 1.910 Fit side-chains outliers start: 26 outliers final: 19 residues processed: 184 average time/residue: 0.2827 time to fit residues: 78.1527 Evaluate side-chains 167 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 148 time to evaluate : 1.786 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1540 time to fit residues: 7.6880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 169 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 ASN D 216 GLN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN D 553 ASN B 41 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 15598 Z= 0.385 Angle : 0.590 8.364 21064 Z= 0.311 Chirality : 0.044 0.174 2286 Planarity : 0.005 0.059 2694 Dihedral : 4.681 30.334 2074 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.79 % Favored : 89.21 % Rotamer: Outliers : 1.97 % Allowed : 15.07 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.20), residues: 1862 helix: 1.11 (0.18), residues: 856 sheet: -1.63 (0.36), residues: 184 loop : -2.74 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 110 HIS 0.008 0.001 HIS B 323 PHE 0.029 0.002 PHE D 550 TYR 0.034 0.002 TYR D 301 ARG 0.007 0.001 ARG B 387 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 166 time to evaluate : 1.815 Fit side-chains outliers start: 33 outliers final: 14 residues processed: 191 average time/residue: 0.2819 time to fit residues: 80.7070 Evaluate side-chains 168 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 154 time to evaluate : 1.712 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1454 time to fit residues: 6.1328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 0.0370 chunk 102 optimal weight: 2.9990 chunk 2 optimal weight: 0.0040 chunk 133 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 153 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 161 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 overall best weight: 0.5870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 284 ASN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN ** A 868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15598 Z= 0.140 Angle : 0.482 7.690 21064 Z= 0.254 Chirality : 0.039 0.178 2286 Planarity : 0.004 0.060 2694 Dihedral : 4.185 26.556 2074 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 0.72 % Allowed : 16.93 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.20), residues: 1862 helix: 1.55 (0.18), residues: 858 sheet: -1.05 (0.39), residues: 164 loop : -2.47 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1026 HIS 0.003 0.001 HIS A 868 PHE 0.030 0.001 PHE B 550 TYR 0.013 0.001 TYR B 301 ARG 0.007 0.000 ARG B 387 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 174 time to evaluate : 1.904 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 182 average time/residue: 0.2839 time to fit residues: 77.2664 Evaluate side-chains 152 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 148 time to evaluate : 1.839 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1577 time to fit residues: 3.7514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 105 optimal weight: 0.0870 chunk 44 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 overall best weight: 2.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 999 ASN D 216 GLN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN ** A 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15598 Z= 0.344 Angle : 0.574 7.769 21064 Z= 0.299 Chirality : 0.043 0.199 2286 Planarity : 0.004 0.059 2694 Dihedral : 4.446 28.286 2074 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 1.50 % Allowed : 17.22 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.20), residues: 1862 helix: 1.46 (0.18), residues: 856 sheet: -1.14 (0.37), residues: 182 loop : -2.49 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1026 HIS 0.006 0.001 HIS D 323 PHE 0.027 0.002 PHE D 550 TYR 0.012 0.001 TYR C 738 ARG 0.008 0.001 ARG D 376 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 153 time to evaluate : 1.894 Fit side-chains outliers start: 25 outliers final: 12 residues processed: 164 average time/residue: 0.2820 time to fit residues: 70.0795 Evaluate side-chains 156 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 2.008 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1667 time to fit residues: 6.4490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 151 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 999 ASN D 208 ASN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN ** A 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15598 Z= 0.198 Angle : 0.506 7.713 21064 Z= 0.266 Chirality : 0.040 0.172 2286 Planarity : 0.004 0.059 2694 Dihedral : 4.292 27.301 2074 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 1.02 % Allowed : 17.22 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.20), residues: 1862 helix: 1.59 (0.18), residues: 860 sheet: -0.72 (0.40), residues: 162 loop : -2.38 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1026 HIS 0.002 0.001 HIS B 323 PHE 0.028 0.001 PHE B 550 TYR 0.012 0.001 TYR D 70 ARG 0.005 0.000 ARG C 709 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 158 time to evaluate : 1.746 Fit side-chains outliers start: 17 outliers final: 5 residues processed: 167 average time/residue: 0.2677 time to fit residues: 68.8408 Evaluate side-chains 157 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 152 time to evaluate : 1.911 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1460 time to fit residues: 3.9402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 140 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 999 ASN D 208 ASN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN B 284 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 553 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15598 Z= 0.361 Angle : 0.580 7.976 21064 Z= 0.304 Chirality : 0.043 0.193 2286 Planarity : 0.004 0.059 2694 Dihedral : 4.558 29.395 2074 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 1.02 % Allowed : 17.58 % Favored : 81.40 % 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: -0.65 (0.20), residues: 1862 helix: 1.45 (0.18), residues: 854 sheet: -1.02 (0.37), residues: 182 loop : -2.45 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1026 HIS 0.006 0.001 HIS B 323 PHE 0.027 0.002 PHE D 550 TYR 0.024 0.002 TYR B 301 ARG 0.009 0.001 ARG D 376 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 153 time to evaluate : 2.110 Fit side-chains outliers start: 17 outliers final: 5 residues processed: 162 average time/residue: 0.2854 time to fit residues: 70.8244 Evaluate side-chains 152 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 147 time to evaluate : 1.820 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1436 time to fit residues: 3.8337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 chunk 167 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 999 ASN D 284 ASN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN B 284 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15598 Z= 0.216 Angle : 0.520 10.843 21064 Z= 0.272 Chirality : 0.040 0.168 2286 Planarity : 0.004 0.059 2694 Dihedral : 4.352 26.278 2074 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 0.60 % Allowed : 17.88 % Favored : 81.52 % 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: -0.41 (0.20), residues: 1862 helix: 1.57 (0.18), residues: 862 sheet: -0.66 (0.40), residues: 162 loop : -2.29 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C1026 HIS 0.003 0.001 HIS D 323 PHE 0.030 0.001 PHE D 145 TYR 0.013 0.001 TYR D 70 ARG 0.005 0.000 ARG C 709 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 160 time to evaluate : 1.856 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 165 average time/residue: 0.2749 time to fit residues: 69.9071 Evaluate side-chains 157 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 152 time to evaluate : 1.780 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1346 time to fit residues: 3.6595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 0.0870 chunk 176 optimal weight: 6.9990 chunk 107 optimal weight: 0.0970 chunk 83 optimal weight: 0.9980 chunk 122 optimal weight: 0.0980 chunk 185 optimal weight: 0.9980 chunk 170 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 999 ASN D 284 ASN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN D 553 ASN B 284 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 15598 Z= 0.133 Angle : 0.484 11.555 21064 Z= 0.253 Chirality : 0.038 0.171 2286 Planarity : 0.004 0.060 2694 Dihedral : 4.015 24.225 2074 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 0.18 % Allowed : 18.24 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.20), residues: 1862 helix: 1.87 (0.18), residues: 856 sheet: -0.54 (0.40), residues: 164 loop : -2.15 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C1026 HIS 0.002 0.001 HIS A 836 PHE 0.024 0.001 PHE D 550 TYR 0.012 0.001 TYR D 70 ARG 0.004 0.000 ARG B 387 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 166 time to evaluate : 1.775 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 167 average time/residue: 0.2819 time to fit residues: 71.2321 Evaluate side-chains 149 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 1.823 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1754 time to fit residues: 2.8356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 5.9990 chunk 157 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 136 optimal weight: 0.0370 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 151 optimal weight: 0.0570 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 855 GLN C 999 ASN D 284 ASN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN D 553 ASN B 284 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.136648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.104921 restraints weight = 21687.560| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.41 r_work: 0.3052 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15598 Z= 0.170 Angle : 0.502 10.117 21064 Z= 0.261 Chirality : 0.039 0.167 2286 Planarity : 0.004 0.059 2694 Dihedral : 3.995 24.747 2074 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 0.12 % Allowed : 18.18 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.20), residues: 1862 helix: 1.83 (0.18), residues: 858 sheet: -0.46 (0.40), residues: 164 loop : -2.12 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1026 HIS 0.003 0.001 HIS A 868 PHE 0.024 0.001 PHE D 550 TYR 0.011 0.001 TYR D 70 ARG 0.007 0.000 ARG B 376 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2913.20 seconds wall clock time: 54 minutes 21.49 seconds (3261.49 seconds total)