Starting phenix.real_space_refine on Sun Mar 17 16:32:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pxv_20522/03_2024/6pxv_20522.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pxv_20522/03_2024/6pxv_20522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pxv_20522/03_2024/6pxv_20522.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pxv_20522/03_2024/6pxv_20522.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pxv_20522/03_2024/6pxv_20522.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pxv_20522/03_2024/6pxv_20522.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 3566 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 120 5.16 5 C 9378 2.51 5 N 2532 2.21 5 O 2744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 19": "NH1" <-> "NH2" Residue "A TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A ARG 331": "NH1" <-> "NH2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "A ARG 554": "NH1" <-> "NH2" Residue "A GLU 633": "OE1" <-> "OE2" Residue "A ARG 717": "NH1" <-> "NH2" Residue "A GLU 754": "OE1" <-> "OE2" Residue "A GLU 755": "OE1" <-> "OE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 760": "OE1" <-> "OE2" Residue "A PHE 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 792": "OE1" <-> "OE2" Residue "A GLU 793": "OE1" <-> "OE2" Residue "A GLU 808": "OE1" <-> "OE2" Residue "A GLU 821": "OE1" <-> "OE2" Residue "A ARG 863": "NH1" <-> "NH2" Residue "A PHE 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 869": "OE1" <-> "OE2" Residue "C ARG 19": "NH1" <-> "NH2" Residue "C TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 270": "NH1" <-> "NH2" Residue "C ARG 331": "NH1" <-> "NH2" Residue "C ARG 386": "NH1" <-> "NH2" Residue "C ARG 554": "NH1" <-> "NH2" Residue "C GLU 633": "OE1" <-> "OE2" Residue "C ARG 717": "NH1" <-> "NH2" Residue "C GLU 754": "OE1" <-> "OE2" Residue "C GLU 755": "OE1" <-> "OE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 760": "OE1" <-> "OE2" Residue "C PHE 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 792": "OE1" <-> "OE2" Residue "C GLU 793": "OE1" <-> "OE2" Residue "C GLU 808": "OE1" <-> "OE2" Residue "C GLU 821": "OE1" <-> "OE2" Residue "C ARG 863": "NH1" <-> "NH2" Residue "C PHE 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 869": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14774 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 823, 6664 Classifications: {'peptide': 823} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 778} Chain breaks: 5 Chain: "C" Number of atoms: 6664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 823, 6664 Classifications: {'peptide': 823} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 778} Chain breaks: 5 Chain: "D" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 376 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Chain: "E" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 376 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Chain: "F" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 347 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain breaks: 1 Chain: "G" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 347 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain breaks: 1 Time building chain proxies: 7.50, per 1000 atoms: 0.51 Number of scatterers: 14774 At special positions: 0 Unit cell: (131.61, 127.33, 176.55, 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 120 16.00 O 2744 8.00 N 2532 7.00 C 9378 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.02 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.04 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.02 Simple disulfide: pdb=" SG CYS A 647 " - pdb=" SG CYS A 860 " distance=2.05 Simple disulfide: pdb=" SG CYS A 786 " - pdb=" SG CYS A 795 " distance=2.05 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS C 26 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 155 " distance=2.03 Simple disulfide: pdb=" SG CYS C 169 " - pdb=" SG CYS C 188 " distance=2.03 Simple disulfide: pdb=" SG CYS C 192 " - pdb=" SG CYS C 201 " distance=2.03 Simple disulfide: pdb=" SG CYS C 196 " - pdb=" SG CYS C 207 " distance=2.03 Simple disulfide: pdb=" SG CYS C 208 " - pdb=" SG CYS C 216 " distance=2.03 Simple disulfide: pdb=" SG CYS C 212 " - pdb=" SG CYS C 225 " distance=2.02 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 241 " - pdb=" SG CYS C 253 " distance=2.03 Simple disulfide: pdb=" SG CYS C 259 " - pdb=" SG CYS C 284 " distance=2.04 Simple disulfide: pdb=" SG CYS C 266 " - pdb=" SG CYS C 274 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 312 " - pdb=" SG CYS C 333 " distance=2.03 Simple disulfide: pdb=" SG CYS C 435 " - pdb=" SG CYS C 468 " distance=2.02 Simple disulfide: pdb=" SG CYS C 647 " - pdb=" SG CYS C 860 " distance=2.05 Simple disulfide: pdb=" SG CYS C 786 " - pdb=" SG CYS C 795 " distance=2.05 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS D 62 " distance=2.04 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 75 " distance=2.02 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 66 " distance=2.03 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS E 62 " distance=2.04 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 75 " distance=2.02 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 66 " distance=2.03 Simple disulfide: pdb=" SG CYS F 7 " - pdb=" SG CYS F 62 " distance=2.04 Simple disulfide: pdb=" SG CYS F 19 " - pdb=" SG CYS F 75 " distance=2.02 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 66 " distance=2.03 Simple disulfide: pdb=" SG CYS G 7 " - pdb=" SG CYS G 62 " distance=2.04 Simple disulfide: pdb=" SG CYS G 19 " - pdb=" SG CYS G 75 " distance=2.02 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 66 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.92 Conformation dependent library (CDL) restraints added in 2.6 seconds 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3448 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 32 sheets defined 17.7% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 18 through 23 removed outlier: 4.080A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.904A pdb=" N PHE A 46 " --> pdb=" O PRO A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.849A pdb=" N CYS A 225 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 264 removed outlier: 3.758A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.666A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 4.059A pdb=" N ARG A 451 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLN A 452 " --> pdb=" O LYS A 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 448 through 452' Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 638 through 643 Processing helix chain 'A' and resid 692 through 714 removed outlier: 3.610A pdb=" N SER A 699 " --> pdb=" O GLU A 695 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 700 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG A 702 " --> pdb=" O GLU A 698 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 703 " --> pdb=" O SER A 699 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 704 " --> pdb=" O SER A 700 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE A 705 " --> pdb=" O PHE A 701 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU A 706 " --> pdb=" O ARG A 702 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A 714 " --> pdb=" O HIS A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 870 Processing helix chain 'C' and resid 18 through 23 removed outlier: 4.080A pdb=" N HIS C 21 " --> pdb=" O THR C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 46 removed outlier: 3.904A pdb=" N PHE C 46 " --> pdb=" O PRO C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 221 through 225 removed outlier: 3.850A pdb=" N CYS C 225 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 264 removed outlier: 3.756A pdb=" N CYS C 259 " --> pdb=" O ASN C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 316 No H-bonds generated for 'chain 'C' and resid 314 through 316' Processing helix chain 'C' and resid 323 through 328 Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 351 through 356 Processing helix chain 'C' and resid 435 through 447 removed outlier: 3.666A pdb=" N ILE C 439 " --> pdb=" O CYS C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 452 removed outlier: 4.060A pdb=" N ARG C 451 " --> pdb=" O THR C 448 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLN C 452 " --> pdb=" O LYS C 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 448 through 452' Processing helix chain 'C' and resid 496 through 498 No H-bonds generated for 'chain 'C' and resid 496 through 498' Processing helix chain 'C' and resid 638 through 643 Processing helix chain 'C' and resid 692 through 714 removed outlier: 3.610A pdb=" N SER C 699 " --> pdb=" O GLU C 695 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER C 700 " --> pdb=" O LEU C 696 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG C 702 " --> pdb=" O GLU C 698 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS C 703 " --> pdb=" O SER C 699 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 704 " --> pdb=" O SER C 700 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE C 705 " --> pdb=" O PHE C 701 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU C 706 " --> pdb=" O ARG C 702 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE C 714 " --> pdb=" O HIS C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 870 Processing helix chain 'D' and resid 7 through 19 Processing helix chain 'D' and resid 57 through 61 Processing helix chain 'D' and resid 67 through 73 removed outlier: 3.639A pdb=" N LEU D 71 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN D 73 " --> pdb=" O TYR D 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 19 Processing helix chain 'E' and resid 57 through 61 Processing helix chain 'E' and resid 67 through 73 removed outlier: 3.639A pdb=" N LEU E 71 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN E 73 " --> pdb=" O TYR E 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 19 Processing helix chain 'F' and resid 57 through 61 Processing helix chain 'F' and resid 67 through 73 removed outlier: 3.640A pdb=" N LEU F 71 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN F 73 " --> pdb=" O TYR F 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 19 Processing helix chain 'G' and resid 57 through 61 Processing helix chain 'G' and resid 67 through 73 removed outlier: 3.639A pdb=" N LEU G 71 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN G 73 " --> pdb=" O TYR G 69 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 14 removed outlier: 6.330A pdb=" N HIS A 32 " --> pdb=" O PRO A 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 14 removed outlier: 6.330A pdb=" N HIS A 32 " --> pdb=" O PRO A 9 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 64 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL A 66 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU A 93 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N GLU A 120 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE A 95 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ASN A 122 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL A 117 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL A 146 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE A 119 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASN A 148 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LYS A 121 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 removed outlier: 3.703A pdb=" N THR A 172 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A 179 " --> pdb=" O THR A 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 231 through 233 Processing sheet with id=AA5, first strand: chain 'A' and resid 252 through 254 removed outlier: 6.863A pdb=" N HIS A 247 " --> pdb=" O CYS A 284 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 292 through 293 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 312 Processing sheet with id=AA8, first strand: chain 'A' and resid 318 through 321 removed outlier: 6.389A pdb=" N ALA A 402 " --> pdb=" O HIS A 429 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 472 through 473 Processing sheet with id=AB1, first strand: chain 'A' and resid 475 through 480 removed outlier: 6.585A pdb=" N ARG A 488 " --> pdb=" O SER A 476 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE A 478 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU A 486 " --> pdb=" O ILE A 478 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 530 through 534 removed outlier: 3.520A pdb=" N ILE A 534 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY A 502 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 599 through 604 removed outlier: 5.070A pdb=" N ASP A 600 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS A 616 " --> pdb=" O ASP A 600 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 759 through 763 removed outlier: 3.876A pdb=" N GLN A 788 " --> pdb=" O ARG A 794 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 759 through 763 Processing sheet with id=AB6, first strand: chain 'A' and resid 819 through 822 Processing sheet with id=AB7, first strand: chain 'A' and resid 857 through 862 removed outlier: 3.591A pdb=" N LEU A 844 " --> pdb=" O THR A 889 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 9 through 14 removed outlier: 6.331A pdb=" N HIS C 32 " --> pdb=" O PRO C 9 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 9 through 14 removed outlier: 6.331A pdb=" N HIS C 32 " --> pdb=" O PRO C 9 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE C 64 " --> pdb=" O ILE C 35 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL C 66 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU C 61 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N PHE C 96 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU C 63 " --> pdb=" O PHE C 96 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU C 93 " --> pdb=" O ARG C 118 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N GLU C 120 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE C 95 " --> pdb=" O GLU C 120 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASN C 122 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL C 117 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL C 146 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE C 119 " --> pdb=" O VAL C 146 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASN C 148 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LYS C 121 " --> pdb=" O ASN C 148 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 171 through 173 removed outlier: 3.703A pdb=" N THR C 172 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 179 " --> pdb=" O THR C 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 231 through 233 Processing sheet with id=AC3, first strand: chain 'C' and resid 252 through 254 removed outlier: 6.863A pdb=" N HIS C 247 " --> pdb=" O CYS C 284 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 292 through 293 Processing sheet with id=AC5, first strand: chain 'C' and resid 311 through 312 Processing sheet with id=AC6, first strand: chain 'C' and resid 318 through 321 removed outlier: 6.388A pdb=" N ALA C 402 " --> pdb=" O HIS C 429 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 472 through 473 Processing sheet with id=AC8, first strand: chain 'C' and resid 475 through 480 removed outlier: 6.586A pdb=" N ARG C 488 " --> pdb=" O SER C 476 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE C 478 " --> pdb=" O LEU C 486 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU C 486 " --> pdb=" O ILE C 478 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 530 through 534 removed outlier: 3.520A pdb=" N ILE C 534 " --> pdb=" O PHE C 503 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY C 502 " --> pdb=" O LEU C 569 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 599 through 604 removed outlier: 5.071A pdb=" N ASP C 600 " --> pdb=" O LYS C 616 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS C 616 " --> pdb=" O ASP C 600 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 759 through 763 removed outlier: 3.876A pdb=" N GLN C 788 " --> pdb=" O ARG C 794 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 759 through 763 Processing sheet with id=AD4, first strand: chain 'C' and resid 819 through 822 Processing sheet with id=AD5, first strand: chain 'C' and resid 857 through 862 removed outlier: 3.591A pdb=" N LEU C 844 " --> pdb=" O THR C 889 " (cutoff:3.500A) 374 hydrogen bonds defined for protein. 930 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: 5.45 Time building geometry restraints manager: 5.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4389 1.34 - 1.46: 3500 1.46 - 1.58: 7091 1.58 - 1.70: 6 1.70 - 1.83: 142 Bond restraints: 15128 Sorted by residual: bond pdb=" CA ASN C 894 " pdb=" C ASN C 894 " ideal model delta sigma weight residual 1.523 1.594 -0.071 1.30e-02 5.92e+03 2.95e+01 bond pdb=" CA ASN A 894 " pdb=" C ASN A 894 " ideal model delta sigma weight residual 1.523 1.593 -0.069 1.30e-02 5.92e+03 2.86e+01 bond pdb=" CG1 ILE A 842 " pdb=" CD1 ILE A 842 " ideal model delta sigma weight residual 1.513 1.310 0.203 3.90e-02 6.57e+02 2.71e+01 bond pdb=" CG1 ILE C 842 " pdb=" CD1 ILE C 842 " ideal model delta sigma weight residual 1.513 1.311 0.202 3.90e-02 6.57e+02 2.67e+01 bond pdb=" CA ASP A 907 " pdb=" C ASP A 907 " ideal model delta sigma weight residual 1.522 1.587 -0.065 1.34e-02 5.57e+03 2.35e+01 ... (remaining 15123 not shown) Histogram of bond angle deviations from ideal: 98.72 - 105.81: 400 105.81 - 112.89: 7497 112.89 - 119.98: 5760 119.98 - 127.07: 6585 127.07 - 134.16: 260 Bond angle restraints: 20502 Sorted by residual: angle pdb=" CA ASN A 881 " pdb=" CB ASN A 881 " pdb=" CG ASN A 881 " ideal model delta sigma weight residual 112.60 119.18 -6.58 1.00e+00 1.00e+00 4.33e+01 angle pdb=" N ALA A 592 " pdb=" CA ALA A 592 " pdb=" C ALA A 592 " ideal model delta sigma weight residual 109.52 119.70 -10.18 1.55e+00 4.16e-01 4.31e+01 angle pdb=" C SER C 639 " pdb=" N GLU C 640 " pdb=" CA GLU C 640 " ideal model delta sigma weight residual 120.28 129.73 -9.45 1.44e+00 4.82e-01 4.30e+01 angle pdb=" CA ASN C 881 " pdb=" CB ASN C 881 " pdb=" CG ASN C 881 " ideal model delta sigma weight residual 112.60 119.15 -6.55 1.00e+00 1.00e+00 4.29e+01 angle pdb=" C SER A 639 " pdb=" N GLU A 640 " pdb=" CA GLU A 640 " ideal model delta sigma weight residual 120.28 129.69 -9.41 1.44e+00 4.82e-01 4.27e+01 ... (remaining 20497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.48: 8658 16.48 - 32.95: 403 32.95 - 49.43: 73 49.43 - 65.91: 28 65.91 - 82.39: 4 Dihedral angle restraints: 9166 sinusoidal: 3820 harmonic: 5346 Sorted by residual: dihedral pdb=" CA THR C 578 " pdb=" C THR C 578 " pdb=" N TYR C 579 " pdb=" CA TYR C 579 " ideal model delta harmonic sigma weight residual 180.00 137.07 42.93 0 5.00e+00 4.00e-02 7.37e+01 dihedral pdb=" CA THR A 578 " pdb=" C THR A 578 " pdb=" N TYR A 579 " pdb=" CA TYR A 579 " ideal model delta harmonic sigma weight residual 180.00 137.09 42.91 0 5.00e+00 4.00e-02 7.36e+01 dihedral pdb=" CB CYS A 266 " pdb=" SG CYS A 266 " pdb=" SG CYS A 274 " pdb=" CB CYS A 274 " ideal model delta sinusoidal sigma weight residual 93.00 149.02 -56.02 1 1.00e+01 1.00e-02 4.24e+01 ... (remaining 9163 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1688 0.088 - 0.177: 402 0.177 - 0.265: 111 0.265 - 0.353: 23 0.353 - 0.442: 4 Chirality restraints: 2228 Sorted by residual: chirality pdb=" CA GLU C 846 " pdb=" N GLU C 846 " pdb=" C GLU C 846 " pdb=" CB GLU C 846 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.88e+00 chirality pdb=" CA GLU A 846 " pdb=" N GLU A 846 " pdb=" C GLU A 846 " pdb=" CB GLU A 846 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" CA VAL A 604 " pdb=" N VAL A 604 " pdb=" C VAL A 604 " pdb=" CB VAL A 604 " both_signs ideal model delta sigma weight residual False 2.44 2.80 -0.36 2.00e-01 2.50e+01 3.23e+00 ... (remaining 2225 not shown) Planarity restraints: 2648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 590 " 0.025 2.00e-02 2.50e+03 5.14e-02 2.64e+01 pdb=" C THR C 590 " -0.089 2.00e-02 2.50e+03 pdb=" O THR C 590 " 0.035 2.00e-02 2.50e+03 pdb=" N ASP C 591 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 590 " -0.024 2.00e-02 2.50e+03 4.99e-02 2.49e+01 pdb=" C THR A 590 " 0.086 2.00e-02 2.50e+03 pdb=" O THR A 590 " -0.034 2.00e-02 2.50e+03 pdb=" N ASP A 591 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 902 " -0.063 2.00e-02 2.50e+03 3.44e-02 2.37e+01 pdb=" CG TYR A 902 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 902 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 TYR A 902 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR A 902 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 902 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR A 902 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 902 " -0.040 2.00e-02 2.50e+03 ... (remaining 2645 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 332 2.68 - 3.24: 12682 3.24 - 3.79: 21913 3.79 - 4.35: 29585 4.35 - 4.90: 49704 Nonbonded interactions: 114216 Sorted by model distance: nonbonded pdb=" CZ PHE C 482 " pdb=" CG2 THR C 593 " model vdw 2.127 3.760 nonbonded pdb=" CE1 PHE C 482 " pdb=" CG2 THR C 593 " model vdw 2.141 3.760 nonbonded pdb=" O THR C 593 " pdb=" O ASN C 594 " model vdw 2.197 3.040 nonbonded pdb=" O THR A 593 " pdb=" O ASN A 594 " model vdw 2.252 3.040 nonbonded pdb=" CE1 PHE A 482 " pdb=" CB THR A 593 " model vdw 2.263 3.770 ... (remaining 114211 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 4 through 26 or resid 56 through 76)) selection = (chain 'E' and (resid 4 through 26 or resid 56 through 76)) selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 6.520 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 39.420 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 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 : 0.010 0.203 15128 Z= 0.677 Angle : 1.391 11.277 20502 Z= 0.845 Chirality : 0.088 0.442 2228 Planarity : 0.009 0.066 2648 Dihedral : 10.112 82.386 5586 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 1.62 % Allowed : 9.33 % Favored : 89.05 % Rotamer: Outliers : 0.36 % Allowed : 3.18 % Favored : 96.46 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.16), residues: 1790 helix: -3.27 (0.24), residues: 240 sheet: -2.34 (0.22), residues: 352 loop : -2.58 (0.15), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.006 TRP A 897 HIS 0.022 0.004 HIS A 829 PHE 0.056 0.005 PHE A 631 TYR 0.064 0.006 TYR C 908 ARG 0.026 0.003 ARG C 885 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 221 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 651 LEU cc_start: 0.3008 (OUTLIER) cc_final: 0.2595 (tt) REVERT: C 651 LEU cc_start: 0.3172 (OUTLIER) cc_final: 0.2732 (tt) outliers start: 6 outliers final: 0 residues processed: 227 average time/residue: 0.3141 time to fit residues: 99.7904 Evaluate side-chains 86 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain C residue 651 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 4.9990 chunk 136 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 32 HIS A 100 HIS A 187 HIS A 209 HIS A 247 HIS A 276 GLN A 328 GLN A 405 ASN A 429 HIS A 546 GLN A 561 GLN A 610 GLN C 15 ASN C 32 HIS C 100 HIS C 187 HIS C 209 HIS C 247 HIS C 276 GLN C 328 GLN C 405 ASN C 429 HIS C 546 GLN C 561 GLN C 610 GLN F 76 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 15128 Z= 0.224 Angle : 0.679 8.378 20502 Z= 0.354 Chirality : 0.045 0.212 2228 Planarity : 0.005 0.051 2648 Dihedral : 6.051 32.791 2004 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.09 % Favored : 92.63 % Rotamer: Outliers : 0.90 % Allowed : 8.76 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.87 (0.18), residues: 1790 helix: -1.95 (0.28), residues: 264 sheet: -1.46 (0.25), residues: 362 loop : -2.14 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 897 HIS 0.005 0.001 HIS A 858 PHE 0.017 0.002 PHE C 903 TYR 0.014 0.002 TYR A 908 ARG 0.004 0.001 ARG A 850 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 1.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 109 average time/residue: 0.2717 time to fit residues: 44.7054 Evaluate side-chains 80 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain C residue 797 VAL Chi-restraints excluded: chain C residue 841 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 136 optimal weight: 0.0470 chunk 111 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 163 optimal weight: 10.0000 chunk 176 optimal weight: 8.9990 chunk 145 optimal weight: 0.6980 chunk 162 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 overall best weight: 2.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN C 410 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 15128 Z= 0.260 Angle : 0.655 13.481 20502 Z= 0.332 Chirality : 0.045 0.148 2228 Planarity : 0.004 0.051 2648 Dihedral : 5.622 31.184 2000 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.10 % Favored : 91.56 % Rotamer: Outliers : 1.20 % Allowed : 9.60 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.35 (0.19), residues: 1790 helix: -1.24 (0.31), residues: 264 sheet: -0.87 (0.26), residues: 362 loop : -1.96 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 897 HIS 0.004 0.001 HIS C 280 PHE 0.018 0.002 PHE A 631 TYR 0.016 0.002 TYR A 430 ARG 0.003 0.000 ARG C 702 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 75 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 70 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7982 (mm-40) outliers start: 20 outliers final: 9 residues processed: 90 average time/residue: 0.2855 time to fit residues: 38.9541 Evaluate side-chains 70 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 841 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 164 optimal weight: 9.9990 chunk 173 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 46 optimal weight: 0.2980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 826 ASN C 826 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15128 Z= 0.231 Angle : 0.596 6.759 20502 Z= 0.308 Chirality : 0.044 0.148 2228 Planarity : 0.004 0.050 2648 Dihedral : 5.383 28.515 2000 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.15 % Favored : 92.51 % Rotamer: Outliers : 1.32 % Allowed : 9.96 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -2.08 (0.20), residues: 1790 helix: -0.75 (0.32), residues: 264 sheet: -0.53 (0.29), residues: 334 loop : -1.89 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 412 HIS 0.004 0.001 HIS C 280 PHE 0.016 0.001 PHE C 903 TYR 0.017 0.001 TYR C 579 ARG 0.006 0.000 ARG C 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 67 time to evaluate : 1.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 837 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6756 (pp20) REVERT: A 854 ASP cc_start: 0.5644 (OUTLIER) cc_final: 0.4487 (t0) REVERT: C 837 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6727 (pp20) outliers start: 22 outliers final: 12 residues processed: 82 average time/residue: 0.2498 time to fit residues: 32.0329 Evaluate side-chains 71 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 56 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 837 GLU Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 837 GLU Chi-restraints excluded: chain C residue 854 ASP Chi-restraints excluded: chain F residue 15 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 120 optimal weight: 0.0010 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 GLN ** C 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15128 Z= 0.183 Angle : 0.567 7.138 20502 Z= 0.293 Chirality : 0.043 0.137 2228 Planarity : 0.004 0.049 2648 Dihedral : 5.145 28.805 2000 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.54 % Favored : 92.12 % Rotamer: Outliers : 1.50 % Allowed : 10.38 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.77 (0.20), residues: 1790 helix: -0.35 (0.33), residues: 264 sheet: -0.08 (0.30), residues: 332 loop : -1.81 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 412 HIS 0.003 0.001 HIS C 280 PHE 0.015 0.001 PHE C 903 TYR 0.014 0.001 TYR A 579 ARG 0.002 0.000 ARG A 863 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 63 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 837 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6833 (pp20) REVERT: A 883 SER cc_start: 0.4547 (OUTLIER) cc_final: 0.4009 (m) REVERT: C 800 TYR cc_start: 0.7401 (m-80) cc_final: 0.7138 (m-10) REVERT: C 837 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6809 (pp20) outliers start: 25 outliers final: 9 residues processed: 83 average time/residue: 0.2704 time to fit residues: 34.0736 Evaluate side-chains 69 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 837 GLU Chi-restraints excluded: chain A residue 883 SER Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 837 GLU Chi-restraints excluded: chain F residue 15 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 4.9990 chunk 156 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 263 HIS A 276 GLN A 541 ASN A 826 ASN A 894 ASN C 263 HIS C 276 GLN C 541 ASN C 826 ASN C 894 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 15128 Z= 0.422 Angle : 0.757 10.531 20502 Z= 0.387 Chirality : 0.047 0.200 2228 Planarity : 0.005 0.065 2648 Dihedral : 5.863 26.219 2000 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.39 % Favored : 89.27 % Rotamer: Outliers : 1.50 % Allowed : 10.62 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -2.02 (0.20), residues: 1790 helix: -0.20 (0.33), residues: 264 sheet: -0.74 (0.29), residues: 360 loop : -1.91 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 832 HIS 0.008 0.002 HIS A 710 PHE 0.020 0.002 PHE C 903 TYR 0.020 0.002 TYR A 579 ARG 0.005 0.001 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 52 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 837 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6673 (pp20) REVERT: C 837 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6668 (pp20) outliers start: 25 outliers final: 15 residues processed: 73 average time/residue: 0.2274 time to fit residues: 27.1782 Evaluate side-chains 60 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 43 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 831 MET Chi-restraints excluded: chain A residue 837 GLU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 831 MET Chi-restraints excluded: chain C residue 837 GLU Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 854 ASP Chi-restraints excluded: chain F residue 15 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.0270 chunk 19 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 chunk 146 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.0042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 HIS ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 627 HIS F 60 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.5225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15128 Z= 0.160 Angle : 0.589 7.783 20502 Z= 0.302 Chirality : 0.043 0.137 2228 Planarity : 0.004 0.076 2648 Dihedral : 5.304 29.068 2000 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.76 % Favored : 92.91 % Rotamer: Outliers : 1.02 % Allowed : 11.34 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.71 (0.20), residues: 1790 helix: 0.10 (0.34), residues: 264 sheet: -0.32 (0.29), residues: 346 loop : -1.79 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 412 HIS 0.002 0.001 HIS C 548 PHE 0.020 0.001 PHE A 903 TYR 0.025 0.001 TYR A 430 ARG 0.004 0.000 ARG A 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 54 time to evaluate : 1.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 837 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6778 (pp20) REVERT: A 854 ASP cc_start: 0.5514 (OUTLIER) cc_final: 0.4926 (t0) REVERT: C 38 MET cc_start: 0.8513 (mmm) cc_final: 0.8113 (mmp) REVERT: C 837 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6796 (pp20) REVERT: C 854 ASP cc_start: 0.5529 (OUTLIER) cc_final: 0.4972 (t0) REVERT: F 22 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7404 (ptt90) outliers start: 17 outliers final: 9 residues processed: 67 average time/residue: 0.2726 time to fit residues: 28.6644 Evaluate side-chains 63 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 49 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 837 GLU Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 837 GLU Chi-restraints excluded: chain C residue 854 ASP Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 22 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 136 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.5651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15128 Z= 0.358 Angle : 0.680 7.011 20502 Z= 0.347 Chirality : 0.045 0.144 2228 Planarity : 0.004 0.047 2648 Dihedral : 5.577 26.311 2000 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.22 % Favored : 89.44 % Rotamer: Outliers : 0.90 % Allowed : 11.46 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.84 (0.20), residues: 1790 helix: 0.17 (0.34), residues: 262 sheet: -0.66 (0.29), residues: 350 loop : -1.83 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 412 HIS 0.006 0.001 HIS A 710 PHE 0.019 0.002 PHE A 903 TYR 0.034 0.002 TYR C 430 ARG 0.006 0.001 ARG F 22 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 43 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 837 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6850 (pp20) REVERT: A 854 ASP cc_start: 0.5479 (OUTLIER) cc_final: 0.4859 (t0) REVERT: C 38 MET cc_start: 0.8715 (mmm) cc_final: 0.8366 (mmp) REVERT: C 837 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6849 (pp20) REVERT: C 854 ASP cc_start: 0.5721 (OUTLIER) cc_final: 0.5086 (t0) REVERT: G 26 TYR cc_start: 0.5499 (OUTLIER) cc_final: 0.4374 (t80) outliers start: 15 outliers final: 7 residues processed: 56 average time/residue: 0.2350 time to fit residues: 22.1457 Evaluate side-chains 51 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 39 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 837 GLU Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 837 GLU Chi-restraints excluded: chain C residue 854 ASP Chi-restraints excluded: chain G residue 26 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 9.9990 chunk 166 optimal weight: 0.0970 chunk 151 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 152 optimal weight: 0.3980 chunk 106 optimal weight: 0.8980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 548 HIS ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.5707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15128 Z= 0.183 Angle : 0.596 8.918 20502 Z= 0.304 Chirality : 0.043 0.136 2228 Planarity : 0.004 0.046 2648 Dihedral : 5.274 28.186 2000 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.32 % Favored : 92.35 % Rotamer: Outliers : 1.02 % Allowed : 11.64 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.74 (0.20), residues: 1790 helix: 0.20 (0.34), residues: 266 sheet: -0.55 (0.29), residues: 336 loop : -1.76 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 412 HIS 0.003 0.001 HIS C 710 PHE 0.020 0.001 PHE A 903 TYR 0.023 0.001 TYR C 430 ARG 0.006 0.000 ARG F 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 48 time to evaluate : 1.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 837 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6899 (pp20) REVERT: A 854 ASP cc_start: 0.5209 (OUTLIER) cc_final: 0.4632 (t0) REVERT: C 38 MET cc_start: 0.8579 (mmm) cc_final: 0.8198 (mmp) REVERT: C 837 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6896 (pp20) REVERT: C 854 ASP cc_start: 0.5327 (OUTLIER) cc_final: 0.4891 (t0) REVERT: G 26 TYR cc_start: 0.5288 (OUTLIER) cc_final: 0.4044 (t80) REVERT: G 72 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8012 (mt-10) outliers start: 17 outliers final: 10 residues processed: 62 average time/residue: 0.2416 time to fit residues: 24.3633 Evaluate side-chains 57 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 42 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 594 ASN Chi-restraints excluded: chain A residue 837 GLU Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain C residue 553 MET Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 594 ASN Chi-restraints excluded: chain C residue 837 GLU Chi-restraints excluded: chain C residue 854 ASP Chi-restraints excluded: chain G residue 26 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.9019 > 50: distance: 78 - 80: 8.653 distance: 80 - 81: 10.470 distance: 81 - 82: 19.552 distance: 81 - 84: 14.251 distance: 82 - 83: 19.316 distance: 82 - 89: 16.264 distance: 84 - 85: 12.515 distance: 85 - 86: 20.444 distance: 86 - 87: 5.694 distance: 86 - 88: 17.068 distance: 89 - 90: 24.190 distance: 90 - 91: 22.806 distance: 90 - 93: 18.498 distance: 91 - 92: 12.518 distance: 91 - 100: 14.918 distance: 93 - 94: 32.443 distance: 94 - 95: 26.899 distance: 95 - 96: 14.852 distance: 96 - 97: 9.082 distance: 97 - 99: 19.682 distance: 100 - 101: 28.325 distance: 101 - 102: 6.504 distance: 102 - 103: 13.736 distance: 102 - 104: 42.901 distance: 104 - 105: 16.266 distance: 105 - 106: 16.430 distance: 105 - 108: 31.560 distance: 106 - 107: 15.424 distance: 106 - 115: 7.551 distance: 108 - 109: 11.542 distance: 109 - 110: 24.923 distance: 109 - 111: 24.201 distance: 110 - 112: 30.037 distance: 111 - 113: 24.121 distance: 112 - 114: 29.717 distance: 115 - 116: 7.342 distance: 116 - 117: 20.258 distance: 116 - 119: 24.317 distance: 117 - 118: 14.535 distance: 117 - 126: 11.281 distance: 120 - 121: 6.819 distance: 120 - 122: 12.318 distance: 121 - 123: 5.837 distance: 122 - 124: 7.176 distance: 123 - 125: 12.378 distance: 124 - 125: 8.186 distance: 126 - 127: 27.700 distance: 127 - 128: 14.912 distance: 127 - 130: 16.798 distance: 128 - 129: 28.304 distance: 128 - 138: 21.657 distance: 130 - 131: 7.591 distance: 131 - 132: 6.931 distance: 131 - 133: 25.323 distance: 132 - 134: 12.935 distance: 133 - 135: 18.457 distance: 134 - 136: 20.691 distance: 135 - 136: 6.282 distance: 136 - 137: 21.157 distance: 138 - 139: 16.800 distance: 139 - 140: 18.161 distance: 139 - 142: 29.793 distance: 140 - 141: 3.928 distance: 140 - 145: 9.289 distance: 142 - 143: 12.843 distance: 142 - 144: 9.230 distance: 145 - 146: 38.400 distance: 145 - 151: 36.066 distance: 146 - 149: 33.183 distance: 147 - 148: 50.172 distance: 149 - 150: 20.372 distance: 150 - 151: 21.818 distance: 152 - 153: 16.142 distance: 153 - 154: 16.421 distance: 154 - 155: 10.234 distance: 154 - 156: 9.712 distance: 156 - 157: 9.122 distance: 157 - 158: 28.180 distance: 157 - 160: 18.635 distance: 158 - 159: 17.222 distance: 158 - 164: 9.064 distance: 159 - 187: 25.230 distance: 160 - 161: 10.375 distance: 160 - 162: 29.039 distance: 161 - 163: 5.432