Starting phenix.real_space_refine on Fri Aug 9 07:13:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tnl_41422/08_2024/8tnl_41422.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tnl_41422/08_2024/8tnl_41422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tnl_41422/08_2024/8tnl_41422.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tnl_41422/08_2024/8tnl_41422.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tnl_41422/08_2024/8tnl_41422.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tnl_41422/08_2024/8tnl_41422.cif" } resolution = 3.62 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= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11118 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 10292 2.51 5 N 2839 2.21 5 O 3251 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 16": "OE1" <-> "OE2" Residue "H TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 17": "OE1" <-> "OE2" Residue "L TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 71": "OE1" <-> "OE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 393": "OE1" <-> "OE2" Residue "C GLU 424": "OE1" <-> "OE2" Residue "C TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 71": "OE1" <-> "OE2" Residue "I TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 336": "OE1" <-> "OE2" Residue "I GLU 385": "OE1" <-> "OE2" Residue "I GLU 393": "OE1" <-> "OE2" Residue "I ASP 437": "OD1" <-> "OD2" Residue "I PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 486": "OE1" <-> "OE2" Residue "K ASP 85": "OD1" <-> "OD2" Residue "K GLU 104": "OE1" <-> "OE2" Residue "K GLU 269": "OE1" <-> "OE2" Residue "K TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 385": "OE1" <-> "OE2" Residue "K GLU 435": "OE1" <-> "OE2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "E PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 87": "OD1" <-> "OD2" Residue "A GLU 16": "OE1" <-> "OE2" Residue "A TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 16478 Number of models: 1 Model: "" Number of chains: 12 Chain: "H" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 907 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "L" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 854 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 102} Chain: "C" Number of atoms: 3699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3699 Classifications: {'peptide': 473} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 459} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "I" Number of atoms: 3699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3699 Classifications: {'peptide': 473} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 459} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "K" Number of atoms: 3699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3699 Classifications: {'peptide': 473} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 459} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 907 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "E" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 854 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 102} Chain: "A" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 907 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "B" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 854 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 102} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.73, per 1000 atoms: 0.53 Number of scatterers: 16478 At special positions: 0 Unit cell: (135.29, 137.78, 161.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 3251 8.00 N 2839 7.00 C 10292 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=25, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 458 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS I 368 " distance=2.05 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 268 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 66 " distance=2.03 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 129 " distance=2.03 Simple disulfide: pdb=" SG CYS C 272 " - pdb=" SG CYS C 296 " distance=2.03 Simple disulfide: pdb=" SG CYS C 465 " - pdb=" SG CYS C 469 " distance=2.03 Simple disulfide: pdb=" SG CYS I 4 " - pdb=" SG CYS I 458 " distance=2.03 Simple disulfide: pdb=" SG CYS I 42 " - pdb=" SG CYS I 268 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 66 " distance=2.03 Simple disulfide: pdb=" SG CYS I 87 " - pdb=" SG CYS I 129 " distance=2.03 Simple disulfide: pdb=" SG CYS I 272 " - pdb=" SG CYS I 296 " distance=2.03 Simple disulfide: pdb=" SG CYS I 465 " - pdb=" SG CYS I 469 " distance=2.03 Simple disulfide: pdb=" SG CYS K 4 " - pdb=" SG CYS K 458 " distance=2.04 Simple disulfide: pdb=" SG CYS K 42 " - pdb=" SG CYS K 268 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 66 " distance=2.03 Simple disulfide: pdb=" SG CYS K 87 " - pdb=" SG CYS K 129 " distance=2.03 Simple disulfide: pdb=" SG CYS K 272 " - pdb=" SG CYS K 296 " distance=2.03 Simple disulfide: pdb=" SG CYS K 465 " - pdb=" SG CYS K 469 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 93 " distance=2.04 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 93 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C 601 " - " ASN C 28 " " NAG C 602 " - " ASN C 403 " " NAG C 603 " - " ASN C 231 " " NAG I 601 " - " ASN I 403 " " NAG I 602 " - " ASN I 28 " " NAG K 601 " - " ASN K 403 " " NAG K 602 " - " ASN K 28 " Time building additional restraints: 6.06 Conformation dependent library (CDL) restraints added in 3.2 seconds 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3822 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 60 sheets defined 19.0% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.23 Creating SS restraints... Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'L' and resid 84 through 88 removed outlier: 3.538A pdb=" N ASP L 87 " --> pdb=" O GLU L 84 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL L 88 " --> pdb=" O ALA L 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 84 through 88' Processing helix chain 'C' and resid 57 through 62 removed outlier: 4.010A pdb=" N THR C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 67 removed outlier: 4.127A pdb=" N ASP C 67 " --> pdb=" O PRO C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 104 Processing helix chain 'C' and resid 178 through 186 Processing helix chain 'C' and resid 358 through 377 removed outlier: 3.946A pdb=" N LYS C 372 " --> pdb=" O CYS C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 448 removed outlier: 3.644A pdb=" N ILE C 429 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 451 No H-bonds generated for 'chain 'C' and resid 449 through 451' Processing helix chain 'C' and resid 466 through 475 Processing helix chain 'I' and resid 57 through 62 removed outlier: 4.268A pdb=" N THR I 61 " --> pdb=" O LEU I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 67 removed outlier: 4.251A pdb=" N ASP I 67 " --> pdb=" O PRO I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 104 removed outlier: 3.973A pdb=" N GLU I 104 " --> pdb=" O GLN I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 186 Processing helix chain 'I' and resid 359 through 377 removed outlier: 4.635A pdb=" N LYS I 372 " --> pdb=" O CYS I 368 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 448 Processing helix chain 'I' and resid 466 through 475 Processing helix chain 'I' and resid 479 through 488 removed outlier: 4.175A pdb=" N TYR I 483 " --> pdb=" O ASP I 479 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLU I 485 " --> pdb=" O SER I 481 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLU I 486 " --> pdb=" O LYS I 482 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 62 removed outlier: 3.771A pdb=" N THR K 61 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 67 removed outlier: 4.088A pdb=" N ASP K 67 " --> pdb=" O PRO K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 104 removed outlier: 3.971A pdb=" N GLU K 104 " --> pdb=" O GLN K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 187 Processing helix chain 'K' and resid 359 through 377 Processing helix chain 'K' and resid 395 through 447 Processing helix chain 'K' and resid 466 through 475 Processing helix chain 'K' and resid 483 through 490 removed outlier: 3.841A pdb=" N ALA K 487 " --> pdb=" O TYR K 483 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN K 490 " --> pdb=" O GLU K 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.643A pdb=" N LYS D 65 " --> pdb=" O PRO D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 88 through 92 removed outlier: 3.570A pdb=" N THR D 92 " --> pdb=" O ALA D 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.601A pdb=" N ASP E 87 " --> pdb=" O GLU E 84 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL E 88 " --> pdb=" O ALA E 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 84 through 88' Processing helix chain 'A' and resid 61 through 64 removed outlier: 3.640A pdb=" N LYS A 64 " --> pdb=" O PRO A 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'B' and resid 84 through 88 removed outlier: 3.614A pdb=" N ASP B 87 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL B 88 " --> pdb=" O ALA B 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 84 through 88' Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA3, first strand: chain 'H' and resid 18 through 19 Processing sheet with id=AA4, first strand: chain 'H' and resid 34 through 35 removed outlier: 3.682A pdb=" N TYR H 50 " --> pdb=" O SER H 58 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER H 58 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 92 through 93 Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.514A pdb=" N THR L 5 " --> pdb=" O ASN L 24 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 58 through 59 removed outlier: 6.212A pdb=" N LEU L 51 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU L 42 " --> pdb=" O LEU L 51 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 89 through 91 removed outlier: 3.650A pdb=" N GLY L 89 " --> pdb=" O VAL L 109 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 355 through 357 removed outlier: 3.572A pdb=" N GLY C 344 " --> pdb=" O GLY C 6 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY C 6 " --> pdb=" O GLY C 344 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 14 through 17 Processing sheet with id=AB2, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AB3, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AB4, first strand: chain 'C' and resid 40 through 42 removed outlier: 5.685A pdb=" N ILE C 41 " --> pdb=" O ASP C 265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 48 through 50 removed outlier: 3.610A pdb=" N ILE C 78 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE C 77 " --> pdb=" O ILE C 258 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 90 through 92 removed outlier: 7.016A pdb=" N LYS C 91 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N TRP C 225 " --> pdb=" O LYS C 91 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 108 through 109 Processing sheet with id=AB8, first strand: chain 'C' and resid 126 through 130 removed outlier: 4.481A pdb=" N CYS C 129 " --> pdb=" O SER C 135 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 140 through 142 removed outlier: 3.503A pdb=" N LYS C 141 " --> pdb=" O ALA C 244 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 155 through 157 removed outlier: 3.549A pdb=" N MET C 155 " --> pdb=" O PHE C 238 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 277 through 279 removed outlier: 3.726A pdb=" N ILE C 279 " --> pdb=" O CYS C 272 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N CYS C 272 " --> pdb=" O ILE C 279 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.968A pdb=" N GLY I 6 " --> pdb=" O GLY I 344 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY I 344 " --> pdb=" O GLY I 6 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS I 347 " --> pdb=" O GLY I 354 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLY I 354 " --> pdb=" O HIS I 347 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 14 through 16 Processing sheet with id=AC5, first strand: chain 'I' and resid 30 through 31 Processing sheet with id=AC6, first strand: chain 'I' and resid 33 through 34 Processing sheet with id=AC7, first strand: chain 'I' and resid 41 through 42 removed outlier: 5.765A pdb=" N ILE I 41 " --> pdb=" O ASP I 265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'I' and resid 48 through 50 removed outlier: 6.255A pdb=" N ILE I 77 " --> pdb=" O ILE I 258 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 108 through 112 Processing sheet with id=AD1, first strand: chain 'I' and resid 140 through 142 removed outlier: 8.510A pdb=" N VAL I 170 " --> pdb=" O PRO I 245 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 203 through 204 Processing sheet with id=AD3, first strand: chain 'I' and resid 273 through 274 Processing sheet with id=AD4, first strand: chain 'I' and resid 451 through 453 Processing sheet with id=AD5, first strand: chain 'K' and resid 353 through 357 removed outlier: 3.986A pdb=" N CYS K 4 " --> pdb=" O ARG K 346 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN K 348 " --> pdb=" O LYS K 2 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU K 452 " --> pdb=" O GLU K 460 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 15 through 16 Processing sheet with id=AD7, first strand: chain 'K' and resid 30 through 31 Processing sheet with id=AD8, first strand: chain 'K' and resid 33 through 34 Processing sheet with id=AD9, first strand: chain 'K' and resid 41 through 42 removed outlier: 5.790A pdb=" N ILE K 41 " --> pdb=" O ASP K 265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'K' and resid 48 through 50 removed outlier: 3.528A pdb=" N ILE K 78 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE K 77 " --> pdb=" O ILE K 258 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 90 through 92 removed outlier: 7.104A pdb=" N LYS K 91 " --> pdb=" O PHE K 223 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N TRP K 225 " --> pdb=" O LYS K 91 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 108 through 112 Processing sheet with id=AE4, first strand: chain 'K' and resid 126 through 130 removed outlier: 4.972A pdb=" N CYS K 129 " --> pdb=" O SER K 135 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 140 through 142 Processing sheet with id=AE6, first strand: chain 'K' and resid 155 through 160 removed outlier: 3.544A pdb=" N TYR K 159 " --> pdb=" O VAL K 234 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 272 through 274 removed outlier: 4.440A pdb=" N CYS K 272 " --> pdb=" O ILE K 279 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY K 277 " --> pdb=" O TYR K 274 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AE9, first strand: chain 'D' and resid 12 through 13 Processing sheet with id=AF1, first strand: chain 'D' and resid 19 through 20 Processing sheet with id=AF2, first strand: chain 'D' and resid 35 through 36 removed outlier: 3.769A pdb=" N TYR D 51 " --> pdb=" O SER D 59 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 72 through 73 Processing sheet with id=AF4, first strand: chain 'D' and resid 94 through 95 Processing sheet with id=AF5, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.550A pdb=" N THR E 5 " --> pdb=" O ASN E 24 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 58 through 59 removed outlier: 5.994A pdb=" N LEU E 51 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU E 42 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE E 53 " --> pdb=" O TRP E 40 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY E 89 " --> pdb=" O VAL E 109 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AF8, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AF9, first strand: chain 'A' and resid 18 through 19 Processing sheet with id=AG1, first strand: chain 'A' and resid 34 through 35 removed outlier: 3.667A pdb=" N TYR A 50 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER A 58 " --> pdb=" O TYR A 50 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'A' and resid 38 through 39 Processing sheet with id=AG3, first strand: chain 'A' and resid 70 through 71 Processing sheet with id=AG4, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AG5, first strand: chain 'B' and resid 58 through 59 removed outlier: 6.219A pdb=" N LEU B 51 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU B 42 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.705A pdb=" N GLY B 89 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 109 " --> pdb=" O GLY B 89 " (cutoff:3.500A) 502 hydrogen bonds defined for protein. 1329 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: 5.04 Time building geometry restraints manager: 6.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4721 1.33 - 1.46: 4497 1.46 - 1.59: 7470 1.59 - 1.72: 0 1.72 - 1.84: 138 Bond restraints: 16826 Sorted by residual: bond pdb=" N TYR C 186 " pdb=" CA TYR C 186 " ideal model delta sigma weight residual 1.458 1.495 -0.038 1.22e-02 6.72e+03 9.59e+00 bond pdb=" N GLN B 95 " pdb=" CA GLN B 95 " ideal model delta sigma weight residual 1.454 1.483 -0.028 1.17e-02 7.31e+03 5.81e+00 bond pdb=" N ARG H 38 " pdb=" CA ARG H 38 " ideal model delta sigma weight residual 1.454 1.482 -0.028 1.18e-02 7.18e+03 5.75e+00 bond pdb=" N LYS K 379 " pdb=" CA LYS K 379 " ideal model delta sigma weight residual 1.453 1.481 -0.029 1.31e-02 5.83e+03 4.82e+00 bond pdb=" C GLN B 47 " pdb=" N SER B 48 " ideal model delta sigma weight residual 1.328 1.359 -0.031 1.44e-02 4.82e+03 4.59e+00 ... (remaining 16821 not shown) Histogram of bond angle deviations from ideal: 99.35 - 106.79: 461 106.79 - 114.23: 9431 114.23 - 121.67: 8567 121.67 - 129.11: 4200 129.11 - 136.55: 124 Bond angle restraints: 22783 Sorted by residual: angle pdb=" C GLY B 16 " pdb=" N GLU B 17 " pdb=" CA GLU B 17 " ideal model delta sigma weight residual 122.56 130.81 -8.25 1.58e+00 4.01e-01 2.72e+01 angle pdb=" CA MET K 470 " pdb=" CB MET K 470 " pdb=" CG MET K 470 " ideal model delta sigma weight residual 114.10 123.85 -9.75 2.00e+00 2.50e-01 2.38e+01 angle pdb=" N GLU K 449 " pdb=" CA GLU K 449 " pdb=" C GLU K 449 " ideal model delta sigma weight residual 114.39 107.39 7.00 1.45e+00 4.76e-01 2.33e+01 angle pdb=" N THR I 477 " pdb=" CA THR I 477 " pdb=" C THR I 477 " ideal model delta sigma weight residual 114.56 109.03 5.53 1.27e+00 6.20e-01 1.90e+01 angle pdb=" CA MET C 470 " pdb=" CB MET C 470 " pdb=" CG MET C 470 " ideal model delta sigma weight residual 114.10 122.30 -8.20 2.00e+00 2.50e-01 1.68e+01 ... (remaining 22778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 9089 18.01 - 36.02: 837 36.02 - 54.02: 154 54.02 - 72.03: 34 72.03 - 90.04: 20 Dihedral angle restraints: 10134 sinusoidal: 4128 harmonic: 6006 Sorted by residual: dihedral pdb=" CB CYS I 272 " pdb=" SG CYS I 272 " pdb=" SG CYS I 296 " pdb=" CB CYS I 296 " ideal model delta sinusoidal sigma weight residual 93.00 11.70 81.30 1 1.00e+01 1.00e-02 8.15e+01 dihedral pdb=" CB CYS C 20 " pdb=" SG CYS C 20 " pdb=" SG CYS I 368 " pdb=" CB CYS I 368 " ideal model delta sinusoidal sigma weight residual 93.00 22.70 70.30 1 1.00e+01 1.00e-02 6.36e+01 dihedral pdb=" CB CYS C 87 " pdb=" SG CYS C 87 " pdb=" SG CYS C 129 " pdb=" CB CYS C 129 " ideal model delta sinusoidal sigma weight residual -86.00 -155.45 69.45 1 1.00e+01 1.00e-02 6.23e+01 ... (remaining 10131 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2229 0.078 - 0.156: 237 0.156 - 0.235: 14 0.235 - 0.313: 2 0.313 - 0.391: 1 Chirality restraints: 2483 Sorted by residual: chirality pdb=" CB ILE C 280 " pdb=" CA ILE C 280 " pdb=" CG1 ILE C 280 " pdb=" CG2 ILE C 280 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" CB VAL I 234 " pdb=" CA VAL I 234 " pdb=" CG1 VAL I 234 " pdb=" CG2 VAL I 234 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA GLU K 424 " pdb=" N GLU K 424 " pdb=" C GLU K 424 " pdb=" CB GLU K 424 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 2480 not shown) Planarity restraints: 2981 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR I 88 " -0.053 5.00e-02 4.00e+02 8.04e-02 1.03e+01 pdb=" N PRO I 89 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO I 89 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO I 89 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 63 " -0.051 5.00e-02 4.00e+02 7.80e-02 9.72e+00 pdb=" N PRO C 64 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO C 64 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 64 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 296 " -0.046 5.00e-02 4.00e+02 6.92e-02 7.66e+00 pdb=" N PRO C 297 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO C 297 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 297 " -0.038 5.00e-02 4.00e+02 ... (remaining 2978 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1567 2.75 - 3.29: 14809 3.29 - 3.83: 27515 3.83 - 4.36: 31003 4.36 - 4.90: 55060 Nonbonded interactions: 129954 Sorted by model distance: nonbonded pdb=" OH TYR H 32 " pdb=" O LEU H 98 " model vdw 2.215 3.040 nonbonded pdb=" OE2 GLU C 111 " pdb=" OH TYR A 52 " model vdw 2.246 3.040 nonbonded pdb=" OG SER C 434 " pdb=" O LEU K 323 " model vdw 2.247 3.040 nonbonded pdb=" O LEU C 323 " pdb=" OG SER I 434 " model vdw 2.261 3.040 nonbonded pdb=" OG1 THR I 18 " pdb=" OE1 GLN I 426 " model vdw 2.280 3.040 ... (remaining 129949 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 'D' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'L' } ncs_group { reference = (chain 'C' and (resid 1 through 490 or resid 601 through 602)) selection = chain 'I' selection = chain 'K' } 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 group one per residue 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: 9.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.420 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 45.000 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 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 : 0.004 0.053 16826 Z= 0.251 Angle : 0.844 15.844 22783 Z= 0.441 Chirality : 0.048 0.391 2483 Planarity : 0.007 0.080 2974 Dihedral : 14.390 90.041 6237 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.06 % Allowed : 0.50 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.98 (0.17), residues: 2082 helix: 0.08 (0.25), residues: 333 sheet: -1.44 (0.23), residues: 565 loop : -1.66 (0.16), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP H 47 HIS 0.008 0.001 HIS H 101 PHE 0.021 0.002 PHE C 136 TYR 0.042 0.002 TYR C 186 ARG 0.012 0.000 ARG I 442 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 376 time to evaluate : 1.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 6 GLN cc_start: 0.5492 (pt0) cc_final: 0.5231 (pt0) REVERT: L 63 VAL cc_start: 0.7774 (t) cc_final: 0.7572 (t) REVERT: I 348 GLN cc_start: 0.8024 (tp40) cc_final: 0.7321 (tp40) REVERT: K 377 ILE cc_start: 0.8276 (mm) cc_final: 0.7990 (mm) REVERT: D 96 TYR cc_start: 0.7367 (m-10) cc_final: 0.7100 (m-10) REVERT: B 2 ILE cc_start: 0.7527 (mt) cc_final: 0.7261 (mt) REVERT: B 63 VAL cc_start: 0.7807 (t) cc_final: 0.7604 (t) outliers start: 1 outliers final: 0 residues processed: 377 average time/residue: 0.2542 time to fit residues: 147.5683 Evaluate side-chains 305 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 8.9990 chunk 156 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 187 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN C 174 HIS ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 239 ASN K 349 ASN K 400 ASN B 43 GLN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16826 Z= 0.226 Angle : 0.616 13.758 22783 Z= 0.314 Chirality : 0.043 0.199 2483 Planarity : 0.005 0.059 2974 Dihedral : 5.812 70.917 2436 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.28 % Allowed : 9.83 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.55 (0.18), residues: 2082 helix: 1.25 (0.28), residues: 333 sheet: -1.50 (0.21), residues: 601 loop : -1.45 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 47 HIS 0.011 0.001 HIS C 174 PHE 0.024 0.001 PHE K 330 TYR 0.020 0.002 TYR I 478 ARG 0.004 0.000 ARG I 484 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 326 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 6 GLN cc_start: 0.6101 (pt0) cc_final: 0.5715 (pt0) REVERT: C 311 MET cc_start: 0.9126 (ppp) cc_final: 0.8497 (ppp) REVERT: I 377 ILE cc_start: 0.8131 (mp) cc_final: 0.7928 (mt) REVERT: K 377 ILE cc_start: 0.8343 (mm) cc_final: 0.8096 (mm) REVERT: K 436 MET cc_start: 0.7472 (tpt) cc_final: 0.7166 (tpt) REVERT: E 4 MET cc_start: 0.6645 (OUTLIER) cc_final: 0.6243 (mmp) REVERT: B 43 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7977 (tt0) outliers start: 23 outliers final: 15 residues processed: 334 average time/residue: 0.2548 time to fit residues: 131.8166 Evaluate side-chains 306 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 289 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 293 VAL Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 293 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain B residue 43 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 188 optimal weight: 0.9980 chunk 203 optimal weight: 7.9990 chunk 167 optimal weight: 0.9990 chunk 186 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 151 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 HIS C 382 GLN I 347 HIS K 400 ASN E 43 GLN B 43 GLN B 95 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16826 Z= 0.255 Angle : 0.602 13.425 22783 Z= 0.306 Chirality : 0.044 0.210 2483 Planarity : 0.005 0.053 2974 Dihedral : 5.602 71.481 2436 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.29 % Allowed : 11.89 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.39 (0.18), residues: 2082 helix: 1.69 (0.28), residues: 333 sheet: -1.54 (0.21), residues: 601 loop : -1.36 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 47 HIS 0.008 0.001 HIS D 54 PHE 0.023 0.002 PHE K 330 TYR 0.020 0.002 TYR C 483 ARG 0.003 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 310 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7930 (mmmt) cc_final: 0.7577 (mmtt) REVERT: C 311 MET cc_start: 0.9083 (ppp) cc_final: 0.8573 (ppp) REVERT: K 377 ILE cc_start: 0.8272 (mm) cc_final: 0.8024 (mm) REVERT: K 444 LYS cc_start: 0.8391 (tptm) cc_final: 0.8124 (tttm) REVERT: E 4 MET cc_start: 0.6648 (mmp) cc_final: 0.6345 (mmp) REVERT: A 111 GLN cc_start: 0.7226 (tp40) cc_final: 0.6857 (mm-40) outliers start: 41 outliers final: 34 residues processed: 324 average time/residue: 0.2705 time to fit residues: 136.8728 Evaluate side-chains 325 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 291 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 293 VAL Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 293 VAL Chi-restraints excluded: chain K residue 388 ASP Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 22 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 188 optimal weight: 0.8980 chunk 200 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 179 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: