Starting phenix.real_space_refine on Mon Jul 22 17:14:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxi_40853/07_2024/8sxi_40853_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxi_40853/07_2024/8sxi_40853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxi_40853/07_2024/8sxi_40853.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxi_40853/07_2024/8sxi_40853.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxi_40853/07_2024/8sxi_40853_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxi_40853/07_2024/8sxi_40853_neut.cif" } resolution = 4.5 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= 0.028 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: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 12123 2.51 5 N 3372 2.21 5 O 3633 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 78": "OD1" <-> "OD2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A GLU 480": "OE1" <-> "OE2" Residue "B PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 624": "OD1" <-> "OD2" Residue "B ASP 632": "OD1" <-> "OD2" Residue "B GLU 647": "OE1" <-> "OE2" Residue "B GLU 648": "OE1" <-> "OE2" Residue "B GLU 657": "OE1" <-> "OE2" Residue "C PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 82": "OD1" <-> "OD2" Residue "D TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 267": "OE1" <-> "OE2" Residue "E GLU 275": "OE1" <-> "OE2" Residue "E GLU 328": "OE1" <-> "OE2" Residue "E GLU 351": "OE1" <-> "OE2" Residue "E PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 464": "OE1" <-> "OE2" Residue "F PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 632": "OD1" <-> "OD2" Residue "F TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 657": "OE1" <-> "OE2" Residue "G PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 1": "OE1" <-> "OE2" Residue "H TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 70": "OD1" <-> "OD2" Residue "H PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 81": "OE1" <-> "OE2" Residue "H TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 83": "OE1" <-> "OE2" Residue "I GLU 91": "OE1" <-> "OE2" Residue "I PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 106": "OE1" <-> "OE2" Residue "I TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 275": "OE1" <-> "OE2" Residue "I TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 328": "OE1" <-> "OE2" Residue "I TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 429": "OE1" <-> "OE2" Residue "I GLU 464": "OE1" <-> "OE2" Residue "I GLU 480": "OE1" <-> "OE2" Residue "J PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 632": "OD1" <-> "OD2" Residue "J TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 659": "OD1" <-> "OD2" Residue "K PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 1": "OE1" <-> "OE2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "L TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 19257 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3569 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 4 Chain: "B" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1001 Classifications: {'peptide': 126} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "C" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1013 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "D" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 836 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "E" Number of atoms: 3569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3569 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 4 Chain: "F" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1001 Classifications: {'peptide': 126} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "G" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1013 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "H" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 836 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "I" Number of atoms: 3569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3569 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 4 Chain: "J" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1001 Classifications: {'peptide': 126} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "K" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1013 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "L" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 836 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Time building chain proxies: 11.18, per 1000 atoms: 0.58 Number of scatterers: 19257 At special positions: 0 Unit cell: (130.226, 137.218, 128.478, 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 129 16.00 O 3633 8.00 N 3372 7.00 C 12123 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS I 167 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 167 " - pdb=" SG CYS E 127 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS A 499 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.04 Simple disulfide: pdb=" SG CYS E 167 " - pdb=" SG CYS I 127 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 499 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.04 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 499 " - pdb=" SG CYS J 605 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 Time building additional restraints: 7.93 Conformation dependent library (CDL) restraints added in 3.6 seconds 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4548 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 49 sheets defined 20.4% alpha, 31.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.84 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 removed outlier: 3.776A pdb=" N GLN A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET A 104 " --> pdb=" O MET A 100 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TRP A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.577A pdb=" N CYS A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 353 removed outlier: 4.108A pdb=" N GLU A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.906A pdb=" N THR A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.652A pdb=" N GLU A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 479 removed outlier: 4.084A pdb=" N TRP A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 484 removed outlier: 4.373A pdb=" N LYS A 483 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.275A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 removed outlier: 3.608A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 664 removed outlier: 3.542A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.761A pdb=" N PHE C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'E' and resid 99 through 117 removed outlier: 3.870A pdb=" N GLN E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TRP E 112 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 127 removed outlier: 4.005A pdb=" N CYS E 127 " --> pdb=" O PRO E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 334 through 353 removed outlier: 4.016A pdb=" N GLU E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TYR E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 392 removed outlier: 4.163A pdb=" N ASN E 392 " --> pdb=" O SER E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.529A pdb=" N GLU E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 479 removed outlier: 3.938A pdb=" N TRP E 477 " --> pdb=" O MET E 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 544 removed outlier: 4.317A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 596 removed outlier: 3.768A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 664 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.914A pdb=" N PHE G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'G' and resid 100E through 100I removed outlier: 3.573A pdb=" N TYR G 100H" --> pdb=" O GLN G 100E" (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR G 100I" --> pdb=" O ASP G 100F" (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 100E through 100I' Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.650A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 117 removed outlier: 3.824A pdb=" N GLN I 103 " --> pdb=" O ASP I 99 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP I 112 " --> pdb=" O VAL I 108 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS I 117 " --> pdb=" O ASP I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 127 removed outlier: 3.988A pdb=" N CYS I 127 " --> pdb=" O PRO I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 334 through 353 removed outlier: 3.947A pdb=" N LYS I 348 " --> pdb=" O ARG I 344 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 removed outlier: 3.700A pdb=" N THR I 372 " --> pdb=" O ASP I 368 " (cutoff:3.500A) Processing helix chain 'I' and resid 387 through 392 removed outlier: 4.049A pdb=" N ASN I 392 " --> pdb=" O SER I 389 " (cutoff:3.500A) Processing helix chain 'I' and resid 425 through 429 removed outlier: 3.700A pdb=" N GLN I 428 " --> pdb=" O ASN I 425 " (cutoff:3.500A) Processing helix chain 'I' and resid 473 through 479 removed outlier: 3.993A pdb=" N TRP I 477 " --> pdb=" O MET I 473 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 534 Processing helix chain 'J' and resid 536 through 544 removed outlier: 4.356A pdb=" N GLN J 540 " --> pdb=" O THR J 536 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU J 544 " --> pdb=" O GLN J 540 " (cutoff:3.500A) Processing helix chain 'J' and resid 572 through 596 removed outlier: 3.788A pdb=" N LEU J 576 " --> pdb=" O GLY J 572 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 636 removed outlier: 3.539A pdb=" N LYS J 633 " --> pdb=" O LEU J 629 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 664 removed outlier: 3.699A pdb=" N ALA J 662 " --> pdb=" O GLN J 658 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.955A pdb=" N PHE K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'K' and resid 100E through 100H removed outlier: 3.756A pdb=" N TYR K 100H" --> pdb=" O GLN K 100E" (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 100E through 100H' Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 492 through 497 removed outlier: 3.853A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.548A pdb=" N LYS A 485 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 132 through 133 removed outlier: 3.577A pdb=" N LYS A 146 " --> pdb=" O PHE A 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 158 through 162 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.405A pdb=" N VAL A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N TYR A 435 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 260 through 261 removed outlier: 6.337A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.712A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.907A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 12.204A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.666A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 359 through 359 Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 274 removed outlier: 10.666A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.204A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.907A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.712A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 443 through 456 current: chain 'A' and resid 414 through 421 removed outlier: 3.619A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 301 through 307 removed outlier: 4.007A pdb=" N GLN A 321A" --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N THR A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N THR A 320 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.714A pdb=" N THR C 77 " --> pdb=" O ASP C 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.865A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 10 through 12 Processing sheet with id=AB5, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.645A pdb=" N VAL D 33 " --> pdb=" O HIS D 49 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N HIS D 49 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TRP D 35 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.518A pdb=" N VAL D 90 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 493 through 497 removed outlier: 4.313A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.715A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC2, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.528A pdb=" N PHE E 93 " --> pdb=" O GLY E 237 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.199A pdb=" N LYS E 168 " --> pdb=" O THR E 163 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 181 through 182 Processing sheet with id=AC5, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.290A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.348A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.646A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.867A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 12.180A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 10.445A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.782A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS E 421 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU E 381 " --> pdb=" O CYS E 378 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 271 through 274 removed outlier: 10.782A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.445A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.180A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 11.867A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.646A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N PHE E 466 " --> pdb=" O ASN E 357 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N THR E 359 " --> pdb=" O PHE E 466 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 301 through 307 removed outlier: 7.147A pdb=" N ASN E 301 " --> pdb=" O VAL E 322 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N VAL E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY E 321 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.623A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR G 77 " --> pdb=" O ASP G 72 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.681A pdb=" N TRP G 36 " --> pdb=" O GLY G 49 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.523A pdb=" N VAL G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AD4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.493A pdb=" N VAL H 33 " --> pdb=" O HIS H 49 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N HIS H 49 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TRP H 35 " --> pdb=" O VAL H 47 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AD6, first strand: chain 'I' and resid 492 through 497 removed outlier: 4.236A pdb=" N VAL I 36 " --> pdb=" O THR J 606 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.584A pdb=" N LYS I 485 " --> pdb=" O LEU I 226 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 53 through 56 Processing sheet with id=AD9, first strand: chain 'I' and resid 84 through 85 Processing sheet with id=AE1, first strand: chain 'I' and resid 130 through 131 Processing sheet with id=AE2, first strand: chain 'I' and resid 145 through 146 Processing sheet with id=AE3, first strand: chain 'I' and resid 181 through 183 Processing sheet with id=AE4, first strand: chain 'I' and resid 201 through 203 removed outlier: 6.428A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET I 434 " --> pdb=" O ILE I 424 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 260 through 261 removed outlier: 6.275A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) removed outlier: 10.632A pdb=" N THR I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.681A pdb=" N ILE I 294 " --> pdb=" O THR I 444 " (cutoff:3.500A) removed outlier: 10.182A pdb=" N ILE I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.447A pdb=" N VAL I 292 " --> pdb=" O ILE I 446 " (cutoff:3.500A) removed outlier: 10.035A pdb=" N ASN I 448 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 10.177A pdb=" N GLU I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU I 295 " --> pdb=" O ASN I 332 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS I 421 " --> pdb=" O PHE I 382 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU I 381 " --> pdb=" O CYS I 378 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 271 through 274 removed outlier: 7.077A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 10.177A pdb=" N GLU I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 10.035A pdb=" N ASN I 448 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 11.447A pdb=" N VAL I 292 " --> pdb=" O ILE I 446 " (cutoff:3.500A) removed outlier: 10.182A pdb=" N ILE I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.681A pdb=" N ILE I 294 " --> pdb=" O THR I 444 " (cutoff:3.500A) removed outlier: 10.632A pdb=" N THR I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASN I 357 " --> pdb=" O GLU I 464 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N PHE I 466 " --> pdb=" O ASN I 357 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N THR I 359 " --> pdb=" O PHE I 466 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 301 through 307 removed outlier: 7.005A pdb=" N ASN I 301 " --> pdb=" O VAL I 322 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N VAL I 322 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.508A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR K 77 " --> pdb=" O ASP K 72 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.481A pdb=" N ILE K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N TRP K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU K 58 " --> pdb=" O TRP K 50 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.958A pdb=" N CYS K 92 " --> pdb=" O TRP K 103 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TRP K 103 " --> pdb=" O CYS K 92 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG K 94 " --> pdb=" O ASP K 101 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.329A pdb=" N VAL L 33 " --> pdb=" O HIS L 49 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N HIS L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 10 through 12 723 hydrogen bonds defined for protein. 1812 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: 6.95 Time building geometry restraints manager: 8.54 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: 6252 1.34 - 1.47: 4809 1.47 - 1.59: 8432 1.59 - 1.72: 1 1.72 - 1.84: 174 Bond restraints: 19668 Sorted by residual: bond pdb=" CA PRO I 437 " pdb=" C PRO I 437 " ideal model delta sigma weight residual 1.517 1.492 0.025 6.70e-03 2.23e+04 1.35e+01 bond pdb=" CB PRO I 76 " pdb=" CG PRO I 76 " ideal model delta sigma weight residual 1.492 1.636 -0.144 5.00e-02 4.00e+02 8.31e+00 bond pdb=" CG1 ILE E 420 " pdb=" CD1 ILE E 420 " ideal model delta sigma weight residual 1.513 1.401 0.112 3.90e-02 6.57e+02 8.19e+00 bond pdb=" CA THR E 372 " pdb=" C THR E 372 " ideal model delta sigma weight residual 1.522 1.485 0.037 1.37e-02 5.33e+03 7.39e+00 bond pdb=" C ASN C 52 " pdb=" N PRO C 52A" ideal model delta sigma weight residual 1.335 1.363 -0.029 1.28e-02 6.10e+03 4.97e+00 ... (remaining 19663 not shown) Histogram of bond angle deviations from ideal: 95.38 - 103.65: 222 103.65 - 111.92: 9093 111.92 - 120.19: 8497 120.19 - 128.46: 8601 128.46 - 136.73: 248 Bond angle restraints: 26661 Sorted by residual: angle pdb=" CA PRO I 76 " pdb=" N PRO I 76 " pdb=" CD PRO I 76 " ideal model delta sigma weight residual 112.00 98.91 13.09 1.40e+00 5.10e-01 8.74e+01 angle pdb=" C GLY B 531 " pdb=" N ALA B 532 " pdb=" CA ALA B 532 " ideal model delta sigma weight residual 121.70 136.29 -14.59 1.80e+00 3.09e-01 6.57e+01 angle pdb=" C GLY J 531 " pdb=" N ALA J 532 " pdb=" CA ALA J 532 " ideal model delta sigma weight residual 121.70 136.19 -14.49 1.80e+00 3.09e-01 6.48e+01 angle pdb=" C ALA F 525 " pdb=" N ALA F 526 " pdb=" CA ALA F 526 " ideal model delta sigma weight residual 121.70 135.86 -14.16 1.80e+00 3.09e-01 6.18e+01 angle pdb=" C ALA B 525 " pdb=" N ALA B 526 " pdb=" CA ALA B 526 " ideal model delta sigma weight residual 121.70 135.82 -14.12 1.80e+00 3.09e-01 6.16e+01 ... (remaining 26656 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 10652 17.98 - 35.96: 969 35.96 - 53.94: 165 53.94 - 71.92: 36 71.92 - 89.90: 25 Dihedral angle restraints: 11847 sinusoidal: 4791 harmonic: 7056 Sorted by residual: dihedral pdb=" CB CYS E 228 " pdb=" SG CYS E 228 " pdb=" SG CYS E 239 " pdb=" CB CYS E 239 " ideal model delta sinusoidal sigma weight residual 93.00 177.74 -84.74 1 1.00e+01 1.00e-02 8.72e+01 dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 170.50 -77.50 1 1.00e+01 1.00e-02 7.52e+01 dihedral pdb=" CB CYS I 228 " pdb=" SG CYS I 228 " pdb=" SG CYS I 239 " pdb=" CB CYS I 239 " ideal model delta sinusoidal sigma weight residual 93.00 166.08 -73.08 1 1.00e+01 1.00e-02 6.81e+01 ... (remaining 11844 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2650 0.094 - 0.188: 290 0.188 - 0.282: 8 0.282 - 0.376: 1 0.376 - 0.470: 3 Chirality restraints: 2952 Sorted by residual: chirality pdb=" CB ILE A 420 " pdb=" CA ILE A 420 " pdb=" CG1 ILE A 420 " pdb=" CG2 ILE A 420 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.53e+00 chirality pdb=" CB ILE A 142 " pdb=" CA ILE A 142 " pdb=" CG1 ILE A 142 " pdb=" CG2 ILE A 142 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" CB ILE E 142 " pdb=" CA ILE E 142 " pdb=" CG1 ILE E 142 " pdb=" CG2 ILE E 142 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.81e+00 ... (remaining 2949 not shown) Planarity restraints: 3408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU I 91 " -0.020 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" CD GLU I 91 " 0.072 2.00e-02 2.50e+03 pdb=" OE1 GLU I 91 " -0.026 2.00e-02 2.50e+03 pdb=" OE2 GLU I 91 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 419 " 0.368 9.50e-02 1.11e+02 1.65e-01 1.71e+01 pdb=" NE ARG E 419 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG E 419 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG E 419 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG E 419 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 35 " 0.009 2.00e-02 2.50e+03 2.19e-02 1.19e+01 pdb=" CG TRP A 35 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP A 35 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP A 35 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 35 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 35 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 35 " 0.020 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 35 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 35 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 35 " -0.002 2.00e-02 2.50e+03 ... (remaining 3405 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 157 2.57 - 3.15: 15832 3.15 - 3.73: 28488 3.73 - 4.32: 38321 4.32 - 4.90: 63423 Nonbonded interactions: 146221 Sorted by model distance: nonbonded pdb=" O ASN E 130 " pdb=" OG SER E 158 " model vdw 1.987 2.440 nonbonded pdb=" O ASN I 130 " pdb=" OG SER I 158 " model vdw 2.021 2.440 nonbonded pdb=" OG1 THR E 257 " pdb=" OG SER E 375 " model vdw 2.072 2.440 nonbonded pdb=" OG SER H 25 " pdb=" OG1 THR H 69 " model vdw 2.092 2.440 nonbonded pdb=" OG1 THR A 257 " pdb=" OG SER A 375 " model vdw 2.112 2.440 ... (remaining 146216 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 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } Set up NCS constraints Number of NCS constrained groups: 4 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } pdb_interpretation.ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } Set refine NCS operators NCS operators will be refined. 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: 2.200 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: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.160 Set scattering table: 0.180 Process input model: 54.600 Find NCS groups from input model: 0.840 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 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 : 0.006 0.144 19668 Z= 0.374 Angle : 1.004 14.587 26661 Z= 0.555 Chirality : 0.056 0.470 2952 Planarity : 0.008 0.165 3408 Dihedral : 14.398 89.903 7173 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.25 % Favored : 93.38 % Rotamer: Outliers : 0.05 % Allowed : 0.19 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -1.44 (0.17), residues: 2385 helix: 0.74 (0.28), residues: 336 sheet: -0.79 (0.19), residues: 627 loop : -1.48 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.004 TRP I 35 HIS 0.011 0.002 HIS L 38 PHE 0.043 0.003 PHE I 93 TYR 0.053 0.003 TYR D 96 ARG 0.031 0.001 ARG E 501 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.8501 (tmm) cc_final: 0.8168 (ttm) REVERT: A 96 TRP cc_start: 0.9099 (m100) cc_final: 0.8707 (m100) REVERT: A 477 TRP cc_start: 0.8590 (m-90) cc_final: 0.8181 (m-90) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1571 time to fit residues: 15.2841 Evaluate side-chains 54 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.436 Evaluate side-chains 49 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 528 SER cc_start: 0.7043 (p) cc_final: 0.6807 (p) REVERT: B 536 THR cc_start: 0.8619 (p) cc_final: 0.8211 (p) REVERT: B 591 GLN cc_start: 0.9140 (tt0) cc_final: 0.8206 (tp40) REVERT: B 607 ASN cc_start: 0.8554 (t0) cc_final: 0.7980 (t0) REVERT: B 649 SER cc_start: 0.8664 (m) cc_final: 0.8403 (m) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0830 time to fit residues: 4.6383 Evaluate side-chains 38 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.104 Evaluate side-chains 41 residues out of total 107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.106 Fit side-chains REVERT: C 36 TRP cc_start: 0.8744 (m100) cc_final: 0.8447 (m100) REVERT: C 48 MET cc_start: 0.8485 (mmm) cc_final: 0.8248 (mmm) REVERT: C 107 THR cc_start: 0.9103 (p) cc_final: 0.8751 (p) outliers start: 1 outliers final: 0 residues processed: 40 average time/residue: 0.1918 time to fit residues: 8.1687 Evaluate side-chains 32 residues out of total 107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.116 Evaluate side-chains 36 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.089 Fit side-chains REVERT: D 35 TRP cc_start: 0.7470 (m100) cc_final: 0.7040 (m-10) REVERT: D 54 ARG cc_start: 0.8060 (mtp-110) cc_final: 0.7765 (mtp180) REVERT: D 103 LYS cc_start: 0.6399 (ttpt) cc_final: 0.5958 (mttt) REVERT: D 104 LEU cc_start: 0.9087 (tt) cc_final: 0.8814 (tt) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.2264 time to fit residues: 8.5422 Evaluate side-chains 26 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 0.0870 chunk 179 optimal weight: 5.9990 chunk 99 optimal weight: 0.0030 chunk 61 optimal weight: 8.9990 chunk 121 optimal weight: 0.0470 chunk 95 optimal weight: 3.9990 chunk 185 optimal weight: 0.0060 chunk 71 optimal weight: 8.9990 chunk 112 optimal weight: 7.9990 chunk 138 optimal weight: 0.0980 chunk 215 optimal weight: 2.9990 overall best weight: 0.0482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 540 GLN J 656 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 53 ASN L 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19668 Z= 0.221 Angle : 0.790 13.089 26661 Z= 0.424 Chirality : 0.050 0.412 2952 Planarity : 0.006 0.113 3408 Dihedral : 6.730 51.812 2634 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.63 % Allowed : 5.66 % Favored : 93.71 % Rotamer: Outliers : 0.70 % Allowed : 4.35 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.03 (0.16), residues: 2385 helix: 0.94 (0.27), residues: 369 sheet: -0.47 (0.19), residues: 657 loop : -1.26 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP E 35 HIS 0.007 0.001 HIS I 249 PHE 0.029 0.003 PHE E 353 TYR 0.052 0.002 TYR L 96 ARG 0.004 0.001 ARG I 169 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 84 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 96 TRP cc_start: 0.9089 (m100) cc_final: 0.8519 (m100) REVERT: A 215 ILE cc_start: 0.7531 (mt) cc_final: 0.7270 (tt) REVERT: A 325 ASP cc_start: 0.7709 (t0) cc_final: 0.7331 (t70) REVERT: A 477 TRP cc_start: 0.7720 (m-90) cc_final: 0.7479 (m-90) outliers start: 3 outliers final: 0 residues processed: 86 average time/residue: 0.1443 time to fit residues: 15.5254 Evaluate side-chains 59 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.448 Evaluate side-chains 44 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.123 Fit side-chains REVERT: J 528 SER cc_start: 0.7689 (p) cc_final: 0.7417 (m) REVERT: J 591 GLN cc_start: 0.8820 (tt0) cc_final: 0.8280 (tp40) REVERT: J 607 ASN cc_start: 0.8498 (t0) cc_final: 0.8035 (t0) REVERT: J 638 TYR cc_start: 0.8414 (m-10) cc_final: 0.7946 (m-10) REVERT: J 655 LYS cc_start: 0.7487 (tppt) cc_final: 0.7241 (tppt) outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 0.0984 time to fit residues: 4.8162 Evaluate side-chains 36 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.104 Evaluate side-chains 40 residues out of total 107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 39 GLN cc_start: 0.6643 (tt0) cc_final: 0.5423 (tt0) REVERT: K 45 PHE cc_start: 0.7872 (m-80) cc_final: 0.5381 (p90) REVERT: K 52 ASN cc_start: 0.8855 (t0) cc_final: 0.8655 (t0) REVERT: K 82 ARG cc_start: 0.6913 (ttm110) cc_final: 0.6212 (mtt90) REVERT: K 82 LEU cc_start: 0.8331 (mp) cc_final: 0.7890 (tp) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1695 time to fit residues: 7.2652 Evaluate side-chains 34 residues out of total 107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.126 Evaluate side-chains 43 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 4 LEU cc_start: 0.6395 (mt) cc_final: 0.5989 (tp) REVERT: L 53 ASN cc_start: 0.7956 (t0) cc_final: 0.7598 (t0) REVERT: L 77 ARG cc_start: 0.8504 (mmm160) cc_final: 0.8111 (ptt180) REVERT: L 87 TYR cc_start: 0.7705 (m-10) cc_final: 0.7494 (m-10) REVERT: L 88 CYS cc_start: 0.3803 (p) cc_final: 0.2415 (p) REVERT: L 96 TYR cc_start: 0.7387 (OUTLIER) cc_final: 0.6651 (p90) REVERT: L 103 LYS cc_start: 0.6834 (ttpt) cc_final: 0.6509 (mttp) REVERT: L 105 GLU cc_start: 0.7039 (pm20) cc_final: 0.6671 (pm20) outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 0.1970 time to fit residues: 8.9593 Evaluate side-chains 36 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 119 optimal weight: 7.9990 chunk 66 optimal weight: 0.5980 chunk 179 optimal weight: 0.0980 chunk 146 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 215 optimal weight: 9.9990 chunk 232 optimal weight: 30.0000 chunk 192 optimal weight: 0.0980 chunk 213 optimal weight: 7.9990 chunk 73 optimal weight: 0.0370 chunk 172 optimal weight: 5.9990 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 287 HIS ** I 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN L 38 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 19668 Z= 0.258 Angle : 0.921 29.650 26661 Z= 0.469 Chirality : 0.055 0.461 2952 Planarity : 0.006 0.055 3408 Dihedral : 6.683 51.757 2634 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.91 % Favored : 93.71 % Rotamer: Outliers : 0.70 % Allowed : 4.49 % Favored : 94.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -1.45 (0.16), residues: 2385 helix: 0.45 (0.26), residues: 366 sheet: -0.76 (0.17), residues: 759 loop : -1.51 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.092 0.005 TRP I 45 HIS 0.015 0.003 HIS I 66 PHE 0.081 0.004 PHE E 93 TYR 0.028 0.002 TYR A 39 ARG 0.012 0.001 ARG A 419 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 66 HIS cc_start: 0.5648 (t-90) cc_final: 0.5322 (t-90) REVERT: I 84 MET cc_start: 0.8561 (tmm) cc_final: 0.8039 (tmm) REVERT: I 293 LYS cc_start: 0.8413 (ttmt) cc_final: 0.8065 (tttp) REVERT: I 480 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8557 (tt0) outliers start: 4 outliers final: 0 residues processed: 76 average time/residue: 0.1375 time to fit residues: 13.3459 Evaluate side-chains 56 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.377 Evaluate side-chains 44 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.101 Fit side-chains revert: symmetry clash REVERT: F 528 SER cc_start: 0.7548 (p) cc_final: 0.7172 (m) REVERT: F 591 GLN cc_start: 0.8797 (tt0) cc_final: 0.8306 (tp40) REVERT: F 592 LEU cc_start: 0.9568 (tp) cc_final: 0.9351 (tp) REVERT: F 607 ASN cc_start: 0.8747 (t0) cc_final: 0.8339 (t0) REVERT: F 626 MET cc_start: 0.6183 (tpt) cc_final: 0.5829 (tpt) REVERT: F 630 GLN cc_start: 0.7952 (mp10) cc_final: 0.7613 (tt0) REVERT: F 638 TYR cc_start: 0.8502 (m-10) cc_final: 0.7938 (m-10) REVERT: F 649 SER cc_start: 0.8854 (m) cc_final: 0.8645 (m) REVERT: F 654 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8407 (mp0) REVERT: F 655 LYS cc_start: 0.7810 (tppt) cc_final: 0.7487 (tppt) REVERT: F 656 ASN cc_start: 0.8789 (m-40) cc_final: 0.8528 (m-40) outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 0.1007 time to fit residues: 4.8629 Evaluate side-chains 38 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.116 Evaluate side-chains 39 residues out of total 107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.112 Fit side-chains revert: symmetry clash REVERT: K 52 ASN cc_start: 0.8645 (t0) cc_final: 0.8425 (t0) REVERT: K 82 ARG cc_start: 0.6917 (ttm110) cc_final: 0.6002 (mtt180) REVERT: K 82 LEU cc_start: 0.8369 (mp) cc_final: 0.7895 (tp) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1932 time to fit residues: 8.0274 Evaluate side-chains 34 residues out of total 107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.106 Evaluate side-chains 39 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.090 Fit side-chains revert: symmetry clash REVERT: L 4 LEU cc_start: 0.6378 (mt) cc_final: 0.6068 (mt) REVERT: L 88 CYS cc_start: 0.3738 (p) cc_final: 0.2674 (p) REVERT: L 103 LYS cc_start: 0.6890 (ttpt) cc_final: 0.6400 (mttt) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1714 time to fit residues: 7.1002 Evaluate side-chains 30 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 213 optimal weight: 20.0000 chunk 162 optimal weight: 40.0000 chunk 111 optimal weight: 0.1980 chunk 23 optimal weight: 0.2980 chunk 102 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 216 optimal weight: 0.0870 chunk 229 optimal weight: 20.0000 chunk 113 optimal weight: 6.9990 chunk 205 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 overall best weight: 1.5160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.276 19668 Z= 0.400 Angle : 0.951 22.488 26661 Z= 0.510 Chirality : 0.055 0.468 2952 Planarity : 0.009 0.185 3408 Dihedral : 6.594 38.921 2634 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.75 % Allowed : 6.67 % Favored : 92.58 % Rotamer: Outliers : 0.28 % Allowed : 4.07 % Favored : 95.65 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -1.80 (0.16), residues: 2385 helix: -0.19 (0.26), residues: 366 sheet: -0.79 (0.18), residues: 720 loop : -1.75 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.094 0.008 TRP I 45 HIS 0.015 0.002 HIS A 66 PHE 0.052 0.004 PHE A 93 TYR 0.071 0.003 TYR H 96 ARG 0.008 0.001 ARG I 419 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 0.418 Fit side-chains REVERT: I 66 HIS cc_start: 0.5748 (t-90) cc_final: 0.5332 (t-90) REVERT: I 293 LYS cc_start: 0.8412 (ttmt) cc_final: 0.8080 (tttp) REVERT: I 480 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8557 (tt0) outliers start: 2 outliers final: 0 residues processed: 75 average time/residue: 0.1495 time to fit residues: 14.0161 Evaluate side-chains 56 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.422 Evaluate side-chains 45 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.118 Fit side-chains revert: symmetry clash REVERT: B 528 SER cc_start: 0.7230 (p) cc_final: 0.6885 (m) REVERT: B 591 GLN cc_start: 0.8890 (tt0) cc_final: 0.8336 (tp40) REVERT: B 607 ASN cc_start: 0.8815 (t0) cc_final: 0.8442 (t0) REVERT: B 626 MET cc_start: 0.6253 (tpt) cc_final: 0.5516 (tpt) REVERT: B 630 GLN cc_start: 0.7965 (mp10) cc_final: 0.7566 (tt0) REVERT: B 638 TYR cc_start: 0.8397 (m-10) cc_final: 0.8011 (m-10) REVERT: B 655 LYS cc_start: 0.7619 (tppt) cc_final: 0.7407 (tppt) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0970 time to fit residues: 4.9091 Evaluate side-chains 37 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.106 Evaluate side-chains 35 residues out of total 107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.104 Fit side-chains REVERT: K 82 ARG cc_start: 0.6739 (ttm110) cc_final: 0.6072 (mtt90) REVERT: K 82 LEU cc_start: 0.8348 (mp) cc_final: 0.7865 (tp) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.2155 time to fit residues: 8.0008 Evaluate side-chains 32 residues out of total 107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.115 Evaluate side-chains 32 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.092 Fit side-chains REVERT: H 4 LEU cc_start: 0.6940 (mt) cc_final: 0.6325 (tp) REVERT: H 11 LEU cc_start: 0.8146 (tp) cc_final: 0.7886 (tt) REVERT: H 30 SER cc_start: 0.7481 (m) cc_final: 0.7224 (p) REVERT: H 35 TRP cc_start: 0.7723 (m-10) cc_final: 0.7312 (m-10) REVERT: H 103 LYS cc_start: 0.6737 (ttpt) cc_final: 0.6478 (mttt) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1304 time to fit residues: 4.5453 Evaluate side-chains 27 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 190 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 170 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 195 optimal weight: 0.0470 chunk 158 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 116 optimal weight: 0.0050 chunk 205 optimal weight: 6.9990 chunk 57 optimal weight: 0.0030 overall best weight: 0.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 476 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.5327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19668 Z= 0.224 Angle : 0.808 11.502 26661 Z= 0.438 Chirality : 0.054 0.529 2952 Planarity : 0.007 0.125 3408 Dihedral : 6.168 30.158 2634 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.63 % Allowed : 6.92 % Favored : 92.45 % Rotamer: Outliers : 0.14 % Allowed : 2.81 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.10 (0.16), residues: 2385 helix: -0.50 (0.27), residues: 357 sheet: -1.01 (0.17), residues: 720 loop : -1.90 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.104 0.007 TRP E 69 HIS 0.015 0.002 HIS A 66 PHE 0.042 0.004 PHE E 93 TYR 0.027 0.002 TYR A 39 ARG 0.005 0.000 ARG A 419 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.445 Fit side-chains REVERT: I 84 MET cc_start: 0.8470 (tmm) cc_final: 0.8050 (ttt) REVERT: I 145 MET cc_start: 0.7609 (mmt) cc_final: 0.7402 (mmm) REVERT: I 190 GLN cc_start: 0.5991 (tt0) cc_final: 0.5733 (tt0) REVERT: I 209 SER cc_start: 0.8611 (t) cc_final: 0.8094 (m) REVERT: I 233 PHE cc_start: 0.8681 (t80) cc_final: 0.8425 (t80) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1339 time to fit residues: 13.4833 Evaluate side-chains 61 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.442 Evaluate side-chains 47 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.121 Fit side-chains REVERT: B 528 SER cc_start: 0.7176 (p) cc_final: 0.6847 (m) REVERT: B 591 GLN cc_start: 0.8848 (tt0) cc_final: 0.8406 (tp40) REVERT: B 607 ASN cc_start: 0.9044 (t0) cc_final: 0.8825 (t0) REVERT: B 614 TRP cc_start: 0.6137 (m-10) cc_final: 0.5905 (m-10) REVERT: B 626 MET cc_start: 0.6046 (tpt) cc_final: 0.5483 (tpt) REVERT: B 630 GLN cc_start: 0.7757 (mp10) cc_final: 0.7488 (tt0) REVERT: B 638 TYR cc_start: 0.8480 (m-10) cc_final: 0.7848 (m-10) REVERT: B 647 GLU cc_start: 0.7822 (tt0) cc_final: 0.7304 (tm-30) REVERT: B 648 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8075 (mm-30) REVERT: B 649 SER cc_start: 0.8917 (m) cc_final: 0.8670 (p) REVERT: B 651 ASN cc_start: 0.8985 (m110) cc_final: 0.7726 (m-40) REVERT: B 655 LYS cc_start: 0.7872 (tppt) cc_final: 0.7626 (tppt) REVERT: B 656 ASN cc_start: 0.8684 (m-40) cc_final: 0.8451 (m110) outliers start: 1 outliers final: 0 residues processed: 46 average time/residue: 0.0992 time to fit residues: 5.1140 Evaluate side-chains 36 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.122 Evaluate side-chains 35 residues out of total 107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.120 Fit side-chains REVERT: K 82 ARG cc_start: 0.6629 (ttm110) cc_final: 0.6101 (mtt90) REVERT: K 82 LEU cc_start: 0.8296 (mp) cc_final: 0.7848 (tp) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1903 time to fit residues: 7.1302 Evaluate side-chains 27 residues out of total 107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.114 Evaluate side-chains 35 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.098 Fit side-chains revert: symmetry clash REVERT: H 4 LEU cc_start: 0.6936 (mt) cc_final: 0.6249 (tp) REVERT: H 35 TRP cc_start: 0.7765 (m-10) cc_final: 0.7366 (m-10) REVERT: H 103 LYS cc_start: 0.6814 (ttpt) cc_final: 0.6435 (mttt) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1567 time to fit residues: 5.8948 Evaluate side-chains 27 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 800, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.1276 > 50: distance: 2 - 3: 4.415 distance: 2 - 5: 8.751 distance: 3 - 4: 10.088 distance: 3 - 8: 3.078 distance: 5 - 6: 10.350 distance: 5 - 7: 9.812 distance: 8 - 9: 5.881 distance: 9 - 10: 4.477 distance: 9 - 12: 13.828 distance: 10 - 11: 7.883 distance: 10 - 16: 16.723 distance: 12 - 13: 26.185 distance: 13 - 14: 11.674 distance: 13 - 15: 8.735 distance: 16 - 17: 13.962 distance: 17 - 18: 15.489 distance: 17 - 20: 14.050 distance: 18 - 19: 42.763 distance: 18 - 24: 11.407 distance: 20 - 21: 14.464 distance: 21 - 22: 17.334 distance: 21 - 23: 32.710 distance: 24 - 25: 11.998 distance: 25 - 26: 25.676 distance: 25 - 28: 20.608 distance: 26 - 27: 20.531 distance: 26 - 30: 20.023 distance: 28 - 29: 8.225 distance: 30 - 31: 5.878 distance: 31 - 32: 39.262 distance: 31 - 34: 12.286 distance: 32 - 33: 12.663 distance: 32 - 37: 36.729 distance: 34 - 35: 12.310 distance: 34 - 36: 29.022 distance: 37 - 38: 45.207 distance: 38 - 39: 42.558 distance: 38 - 41: 26.903 distance: 39 - 40: 10.412 distance: 39 - 45: 6.754 distance: 41 - 42: 13.286 distance: 42 - 43: 5.975 distance: 42 - 44: 7.576 distance: 45 - 46: 19.941 distance: 46 - 47: 3.135 distance: 46 - 49: 11.244 distance: 47 - 48: 4.099 distance: 47 - 50: 11.075 distance: 50 - 51: 19.383 distance: 51 - 52: 9.686 distance: 51 - 54: 12.147 distance: 52 - 53: 3.146 distance: 52 - 57: 7.634 distance: 54 - 55: 3.229 distance: 54 - 56: 15.693 distance: 57 - 58: 14.078 distance: 58 - 59: 13.379 distance: 58 - 61: 5.555 distance: 59 - 60: 11.785 distance: 59 - 62: 13.069 distance: 62 - 63: 7.706 distance: 63 - 64: 21.031 distance: 63 - 66: 31.841 distance: 64 - 65: 9.766 distance: 64 - 68: 24.231 distance: 66 - 67: 22.676 distance: 68 - 69: 43.234 distance: 69 - 70: 25.463 distance: 69 - 72: 21.308 distance: 70 - 71: 21.065 distance: 70 - 76: 12.745 distance: 72 - 73: 12.887 distance: 73 - 74: 15.626 distance: 73 - 75: 9.488 distance: 76 - 77: 8.490 distance: 77 - 78: 10.444 distance: 77 - 80: 9.001 distance: 78 - 79: 5.342 distance: 78 - 82: 9.294 distance: 80 - 81: 10.908 distance: 82 - 83: 8.784 distance: 83 - 84: 7.344