Starting phenix.real_space_refine (version: dev) on Sat Feb 25 02:05:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5k_22682/02_2023/7k5k_22682_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5k_22682/02_2023/7k5k_22682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5k_22682/02_2023/7k5k_22682.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5k_22682/02_2023/7k5k_22682.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5k_22682/02_2023/7k5k_22682_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5k_22682/02_2023/7k5k_22682_updated.pdb" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.016 sd= 0.156 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 Process input model Symmetric amino acids flipped Residue "A GLU 208": "OE1" <-> "OE2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "B GLU 243": "OE1" <-> "OE2" Residue "B GLU 271": "OE1" <-> "OE2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "B GLU 346": "OE1" <-> "OE2" Residue "B GLU 490": "OE1" <-> "OE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "C GLU 115": "OE1" <-> "OE2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C GLU 238": "OE1" <-> "OE2" Residue "C GLU 242": "OE1" <-> "OE2" Residue "C TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 327": "OE1" <-> "OE2" Residue "C GLU 335": "OE1" <-> "OE2" Residue "C GLU 490": "OE1" <-> "OE2" Residue "C GLU 538": "OE1" <-> "OE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "D GLU 238": "OE1" <-> "OE2" Residue "D GLU 242": "OE1" <-> "OE2" Residue "D TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 271": "OE1" <-> "OE2" Residue "D GLU 327": "OE1" <-> "OE2" Residue "D GLU 335": "OE1" <-> "OE2" Residue "D GLU 490": "OE1" <-> "OE2" Residue "D GLU 538": "OE1" <-> "OE2" Residue "E GLU 242": "OE1" <-> "OE2" Residue "E GLU 243": "OE1" <-> "OE2" Residue "E GLU 335": "OE1" <-> "OE2" Residue "E GLU 346": "OE1" <-> "OE2" Residue "E GLU 490": "OE1" <-> "OE2" Residue "E GLU 538": "OE1" <-> "OE2" Residue "F GLU 208": "OE1" <-> "OE2" Residue "F GLU 211": "OE1" <-> "OE2" Residue "F GLU 238": "OE1" <-> "OE2" Residue "F GLU 242": "OE1" <-> "OE2" Residue "F GLU 271": "OE1" <-> "OE2" Residue "F GLU 335": "OE1" <-> "OE2" Residue "F GLU 346": "OE1" <-> "OE2" Residue "F GLU 381": "OE1" <-> "OE2" Residue "F GLU 490": "OE1" <-> "OE2" Residue "F GLU 538": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 24224 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4020 Classifications: {'peptide': 545} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 17, 'TRANS': 527} Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 7, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 88 Chain: "B" Number of atoms: 4044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4044 Classifications: {'peptide': 545} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 17, 'TRANS': 527} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 7, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 79 Chain: "C" Number of atoms: 4056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4056 Classifications: {'peptide': 545} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 17, 'TRANS': 527} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "D" Number of atoms: 4036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4036 Classifications: {'peptide': 545} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 17, 'TRANS': 527} Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 7, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 75 Chain: "E" Number of atoms: 4009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4009 Classifications: {'peptide': 545} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 17, 'TRANS': 527} Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 9, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 94 Chain: "F" Number of atoms: 4023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4023 Classifications: {'peptide': 545} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 17, 'TRANS': 527} Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 7, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 79 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' MN': 2, 'CO3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' MN': 2, 'CO3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' MN': 2, 'CO3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' MN': 2, 'CO3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' MN': 2, 'CO3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' MN': 2, 'CO3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 14.32, per 1000 atoms: 0.59 Number of scatterers: 24224 At special positions: 0 Unit cell: (145.22, 142.04, 96.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 12 24.99 S 89 16.00 O 4651 8.00 N 3986 7.00 C 15486 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 10.50 Conformation dependent library (CDL) restraints added in 3.7 seconds 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6012 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 93 helices and 18 sheets defined 31.3% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'A' and resid 95 through 98 No H-bonds generated for 'chain 'A' and resid 95 through 98' Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 211 through 225 removed outlier: 3.802A pdb=" N LEU A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 257 Processing helix chain 'A' and resid 285 through 287 No H-bonds generated for 'chain 'A' and resid 285 through 287' Processing helix chain 'A' and resid 291 through 310 Processing helix chain 'A' and resid 318 through 332 removed outlier: 3.570A pdb=" N LYS A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 346 removed outlier: 3.616A pdb=" N GLU A 346 " --> pdb=" O LYS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 356 removed outlier: 3.567A pdb=" N VAL A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 356 " --> pdb=" O TYR A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 432 removed outlier: 4.774A pdb=" N LYS A 413 " --> pdb=" O ASP A 410 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP A 415 " --> pdb=" O MET A 412 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N MET A 416 " --> pdb=" O LYS A 413 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N GLY A 418 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE A 432 " --> pdb=" O ILE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 490 Processing helix chain 'A' and resid 505 through 508 removed outlier: 3.540A pdb=" N LEU A 508 " --> pdb=" O GLY A 505 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 505 through 508' Processing helix chain 'A' and resid 523 through 536 removed outlier: 3.616A pdb=" N THR A 535 " --> pdb=" O SER A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 553 Processing helix chain 'A' and resid 570 through 580 removed outlier: 3.632A pdb=" N GLU A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 617 Processing helix chain 'B' and resid 95 through 98 Processing helix chain 'B' and resid 164 through 167 No H-bonds generated for 'chain 'B' and resid 164 through 167' Processing helix chain 'B' and resid 211 through 225 removed outlier: 3.530A pdb=" N THR B 223 " --> pdb=" O TYR B 219 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 257 Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 291 through 310 Processing helix chain 'B' and resid 318 through 332 Processing helix chain 'B' and resid 341 through 346 removed outlier: 3.678A pdb=" N GLU B 346 " --> pdb=" O LYS B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 356 removed outlier: 3.598A pdb=" N VAL B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY B 356 " --> pdb=" O TYR B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 432 removed outlier: 3.506A pdb=" N MET B 412 " --> pdb=" O ILE B 409 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LYS B 413 " --> pdb=" O ASP B 410 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N MET B 416 " --> pdb=" O LYS B 413 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N GLY B 418 " --> pdb=" O ASP B 415 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE B 432 " --> pdb=" O ILE B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 490 Processing helix chain 'B' and resid 505 through 510 removed outlier: 3.634A pdb=" N LEU B 508 " --> pdb=" O GLY B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 536 removed outlier: 3.526A pdb=" N THR B 535 " --> pdb=" O SER B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 553 removed outlier: 3.542A pdb=" N ARG B 550 " --> pdb=" O ASN B 547 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER B 551 " --> pdb=" O GLU B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 580 removed outlier: 3.657A pdb=" N GLU B 580 " --> pdb=" O LEU B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 617 Processing helix chain 'C' and resid 95 through 98 Processing helix chain 'C' and resid 165 through 168 No H-bonds generated for 'chain 'C' and resid 165 through 168' Processing helix chain 'C' and resid 211 through 225 removed outlier: 3.759A pdb=" N LEU C 224 " --> pdb=" O ALA C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 257 Processing helix chain 'C' and resid 285 through 287 No H-bonds generated for 'chain 'C' and resid 285 through 287' Processing helix chain 'C' and resid 291 through 310 Processing helix chain 'C' and resid 318 through 332 Processing helix chain 'C' and resid 341 through 346 removed outlier: 3.608A pdb=" N GLU C 346 " --> pdb=" O LYS C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 356 removed outlier: 3.676A pdb=" N VAL C 355 " --> pdb=" O ALA C 351 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY C 356 " --> pdb=" O TYR C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 432 removed outlier: 4.813A pdb=" N LYS C 413 " --> pdb=" O ASP C 410 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP C 415 " --> pdb=" O MET C 412 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N MET C 416 " --> pdb=" O LYS C 413 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLY C 418 " --> pdb=" O ASP C 415 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE C 432 " --> pdb=" O ILE C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 492 removed outlier: 3.517A pdb=" N LYS C 491 " --> pdb=" O VAL C 487 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 492 " --> pdb=" O TYR C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 508 removed outlier: 3.721A pdb=" N LEU C 508 " --> pdb=" O GLY C 505 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 505 through 508' Processing helix chain 'C' and resid 523 through 536 removed outlier: 3.601A pdb=" N THR C 535 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 553 removed outlier: 3.530A pdb=" N ARG C 550 " --> pdb=" O ASN C 547 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N SER C 551 " --> pdb=" O GLU C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 581 removed outlier: 3.580A pdb=" N GLU C 580 " --> pdb=" O LEU C 576 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE C 581 " --> pdb=" O PHE C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 618 Processing helix chain 'D' and resid 166 through 168 No H-bonds generated for 'chain 'D' and resid 166 through 168' Processing helix chain 'D' and resid 211 through 225 removed outlier: 3.697A pdb=" N LEU D 224 " --> pdb=" O ALA D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 257 Processing helix chain 'D' and resid 285 through 287 No H-bonds generated for 'chain 'D' and resid 285 through 287' Processing helix chain 'D' and resid 291 through 310 Processing helix chain 'D' and resid 318 through 332 Processing helix chain 'D' and resid 341 through 346 removed outlier: 3.612A pdb=" N GLU D 346 " --> pdb=" O LYS D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 356 removed outlier: 3.675A pdb=" N VAL D 355 " --> pdb=" O ALA D 351 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY D 356 " --> pdb=" O TYR D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 432 removed outlier: 4.819A pdb=" N LYS D 413 " --> pdb=" O ASP D 410 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP D 415 " --> pdb=" O MET D 412 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N MET D 416 " --> pdb=" O LYS D 413 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N GLY D 418 " --> pdb=" O ASP D 415 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE D 432 " --> pdb=" O ILE D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 492 removed outlier: 3.507A pdb=" N LYS D 491 " --> pdb=" O VAL D 487 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU D 492 " --> pdb=" O TYR D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 510 removed outlier: 3.720A pdb=" N LEU D 508 " --> pdb=" O GLY D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 536 removed outlier: 3.601A pdb=" N THR D 535 " --> pdb=" O SER D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 553 removed outlier: 4.400A pdb=" N SER D 551 " --> pdb=" O GLU D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 581 removed outlier: 3.592A pdb=" N GLU D 580 " --> pdb=" O LEU D 576 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE D 581 " --> pdb=" O PHE D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 617 Processing helix chain 'E' and resid 95 through 98 No H-bonds generated for 'chain 'E' and resid 95 through 98' Processing helix chain 'E' and resid 144 through 146 No H-bonds generated for 'chain 'E' and resid 144 through 146' Processing helix chain 'E' and resid 211 through 225 removed outlier: 3.512A pdb=" N THR E 223 " --> pdb=" O TYR E 219 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU E 224 " --> pdb=" O ALA E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 257 Processing helix chain 'E' and resid 285 through 287 No H-bonds generated for 'chain 'E' and resid 285 through 287' Processing helix chain 'E' and resid 291 through 310 Processing helix chain 'E' and resid 318 through 332 removed outlier: 3.572A pdb=" N LYS E 331 " --> pdb=" O GLU E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 346 removed outlier: 3.615A pdb=" N GLU E 346 " --> pdb=" O LYS E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 356 removed outlier: 3.567A pdb=" N VAL E 355 " --> pdb=" O ALA E 351 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY E 356 " --> pdb=" O TYR E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 432 removed outlier: 4.801A pdb=" N LYS E 413 " --> pdb=" O ASP E 410 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP E 415 " --> pdb=" O MET E 412 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N MET E 416 " --> pdb=" O LYS E 413 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N GLY E 418 " --> pdb=" O ASP E 415 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE E 432 " --> pdb=" O ILE E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 492 removed outlier: 3.563A pdb=" N LYS E 491 " --> pdb=" O VAL E 487 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU E 492 " --> pdb=" O TYR E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 508 removed outlier: 3.545A pdb=" N LEU E 508 " --> pdb=" O GLY E 505 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 505 through 508' Processing helix chain 'E' and resid 523 through 536 removed outlier: 3.622A pdb=" N THR E 535 " --> pdb=" O SER E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 550 through 553 Processing helix chain 'E' and resid 570 through 581 removed outlier: 3.632A pdb=" N GLU E 580 " --> pdb=" O LEU E 576 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE E 581 " --> pdb=" O PHE E 577 " (cutoff:3.500A) Processing helix chain 'E' and resid 609 through 617 Processing helix chain 'F' and resid 211 through 225 removed outlier: 3.538A pdb=" N THR F 223 " --> pdb=" O TYR F 219 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU F 224 " --> pdb=" O ALA F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 257 Processing helix chain 'F' and resid 285 through 287 No H-bonds generated for 'chain 'F' and resid 285 through 287' Processing helix chain 'F' and resid 291 through 310 Processing helix chain 'F' and resid 318 through 332 Processing helix chain 'F' and resid 341 through 346 removed outlier: 3.676A pdb=" N GLU F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 356 removed outlier: 3.588A pdb=" N VAL F 355 " --> pdb=" O ALA F 351 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY F 356 " --> pdb=" O TYR F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 432 removed outlier: 3.509A pdb=" N MET F 412 " --> pdb=" O ILE F 409 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LYS F 413 " --> pdb=" O ASP F 410 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET F 416 " --> pdb=" O LYS F 413 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLY F 418 " --> pdb=" O ASP F 415 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE F 432 " --> pdb=" O ILE F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 478 through 490 Processing helix chain 'F' and resid 505 through 508 removed outlier: 3.641A pdb=" N LEU F 508 " --> pdb=" O GLY F 505 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 505 through 508' Processing helix chain 'F' and resid 523 through 536 removed outlier: 3.524A pdb=" N THR F 535 " --> pdb=" O SER F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 553 removed outlier: 3.551A pdb=" N ARG F 550 " --> pdb=" O ASN F 547 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER F 551 " --> pdb=" O GLU F 548 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 581 removed outlier: 3.654A pdb=" N GLU F 580 " --> pdb=" O LEU F 576 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE F 581 " --> pdb=" O PHE F 577 " (cutoff:3.500A) Processing helix chain 'F' and resid 609 through 617 Processing sheet with id= A, first strand: chain 'A' and resid 100 through 105 removed outlier: 6.539A pdb=" N LEU A 117 " --> pdb=" O SER A 234 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE A 236 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL A 119 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA A 199 " --> pdb=" O PHE A 120 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N LEU A 122 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL A 201 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 364 through 371 removed outlier: 6.505A pdb=" N LYS A 383 " --> pdb=" O GLU A 438 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N HIS A 440 " --> pdb=" O LYS A 383 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE A 385 " --> pdb=" O HIS A 440 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU A 442 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU A 387 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ALA A 444 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N GLY A 389 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TYR A 496 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ILE A 388 " --> pdb=" O TYR A 496 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL A 498 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ASP A 499 " --> pdb=" O PRO A 586 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA A 588 " --> pdb=" O ASP A 499 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ALA A 501 " --> pdb=" O ALA A 588 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE A 590 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY A 517 " --> pdb=" O ASP A 591 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 460 through 462 Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.842A pdb=" N ALA B 199 " --> pdb=" O PHE B 120 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N LEU B 122 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL B 201 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 364 through 371 removed outlier: 6.456A pdb=" N LYS B 383 " --> pdb=" O GLU B 438 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N HIS B 440 " --> pdb=" O LYS B 383 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE B 385 " --> pdb=" O HIS B 440 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU B 442 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU B 387 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ALA B 444 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N GLY B 389 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TYR B 496 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ILE B 388 " --> pdb=" O TYR B 496 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL B 498 " --> pdb=" O ILE B 388 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ASP B 499 " --> pdb=" O PRO B 586 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA B 588 " --> pdb=" O ASP B 499 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ALA B 501 " --> pdb=" O ALA B 588 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE B 590 " --> pdb=" O ALA B 501 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 460 through 462 Processing sheet with id= G, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.919A pdb=" N ALA C 199 " --> pdb=" O PHE C 120 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N LEU C 122 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL C 201 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 364 through 371 removed outlier: 6.609A pdb=" N LYS C 383 " --> pdb=" O GLU C 438 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N HIS C 440 " --> pdb=" O LYS C 383 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE C 385 " --> pdb=" O HIS C 440 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LEU C 442 " --> pdb=" O ILE C 385 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU C 387 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N ALA C 444 " --> pdb=" O LEU C 387 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N GLY C 389 " --> pdb=" O ALA C 444 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TYR C 496 " --> pdb=" O ALA C 386 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ILE C 388 " --> pdb=" O TYR C 496 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL C 498 " --> pdb=" O ILE C 388 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N ASP C 499 " --> pdb=" O PRO C 586 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA C 588 " --> pdb=" O ASP C 499 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N ALA C 501 " --> pdb=" O ALA C 588 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE C 590 " --> pdb=" O ALA C 501 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY C 517 " --> pdb=" O ASP C 591 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 460 through 462 Processing sheet with id= J, first strand: chain 'D' and resid 100 through 105 removed outlier: 3.510A pdb=" N ILE D 282 " --> pdb=" O LYS D 104 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU D 117 " --> pdb=" O SER D 234 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ILE D 236 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL D 119 " --> pdb=" O ILE D 236 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 364 through 371 removed outlier: 6.596A pdb=" N LYS D 383 " --> pdb=" O GLU D 438 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N HIS D 440 " --> pdb=" O LYS D 383 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE D 385 " --> pdb=" O HIS D 440 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LEU D 442 " --> pdb=" O ILE D 385 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU D 387 " --> pdb=" O LEU D 442 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N ALA D 444 " --> pdb=" O LEU D 387 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N GLY D 389 " --> pdb=" O ALA D 444 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TYR D 496 " --> pdb=" O ALA D 386 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE D 388 " --> pdb=" O TYR D 496 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL D 498 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N ASP D 499 " --> pdb=" O PRO D 586 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA D 588 " --> pdb=" O ASP D 499 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ALA D 501 " --> pdb=" O ALA D 588 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ILE D 590 " --> pdb=" O ALA D 501 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY D 517 " --> pdb=" O ASP D 591 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 460 through 462 Processing sheet with id= M, first strand: chain 'E' and resid 100 through 105 Processing sheet with id= N, first strand: chain 'E' and resid 364 through 371 removed outlier: 6.499A pdb=" N LYS E 383 " --> pdb=" O GLU E 438 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N HIS E 440 " --> pdb=" O LYS E 383 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE E 385 " --> pdb=" O HIS E 440 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LEU E 442 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU E 387 " --> pdb=" O LEU E 442 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ALA E 444 " --> pdb=" O LEU E 387 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N GLY E 389 " --> pdb=" O ALA E 444 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TYR E 496 " --> pdb=" O ALA E 386 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ILE E 388 " --> pdb=" O TYR E 496 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL E 498 " --> pdb=" O ILE E 388 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ASP E 499 " --> pdb=" O PRO E 586 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA E 588 " --> pdb=" O ASP E 499 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ALA E 501 " --> pdb=" O ALA E 588 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE E 590 " --> pdb=" O ALA E 501 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY E 517 " --> pdb=" O ASP E 591 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 460 through 462 Processing sheet with id= P, first strand: chain 'F' and resid 100 through 105 removed outlier: 6.839A pdb=" N ALA F 199 " --> pdb=" O PHE F 120 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LEU F 122 " --> pdb=" O ALA F 199 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL F 201 " --> pdb=" O LEU F 122 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 364 through 371 removed outlier: 6.449A pdb=" N LYS F 383 " --> pdb=" O GLU F 438 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N HIS F 440 " --> pdb=" O LYS F 383 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE F 385 " --> pdb=" O HIS F 440 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N LEU F 442 " --> pdb=" O ILE F 385 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU F 387 " --> pdb=" O LEU F 442 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ALA F 444 " --> pdb=" O LEU F 387 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N GLY F 389 " --> pdb=" O ALA F 444 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TYR F 496 " --> pdb=" O ALA F 386 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ILE F 388 " --> pdb=" O TYR F 496 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL F 498 " --> pdb=" O ILE F 388 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ASP F 499 " --> pdb=" O PRO F 586 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA F 588 " --> pdb=" O ASP F 499 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N ALA F 501 " --> pdb=" O ALA F 588 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE F 590 " --> pdb=" O ALA F 501 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 460 through 462 762 hydrogen bonds defined for protein. 1923 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: 7.87 Time building geometry restraints manager: 11.04 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: 7811 1.34 - 1.46: 4015 1.46 - 1.57: 12717 1.57 - 1.69: 0 1.69 - 1.81: 131 Bond restraints: 24674 Sorted by residual: bond pdb=" CA GLY C 181 " pdb=" C GLY C 181 " ideal model delta sigma weight residual 1.530 1.510 0.020 1.04e-02 9.25e+03 3.76e+00 bond pdb=" N GLY C 181 " pdb=" CA GLY C 181 " ideal model delta sigma weight residual 1.464 1.444 0.021 1.12e-02 7.97e+03 3.38e+00 bond pdb=" C LEU A 83 " pdb=" N ASP A 84 " ideal model delta sigma weight residual 1.331 1.292 0.039 2.83e-02 1.25e+03 1.89e+00 bond pdb=" C CYS A 111 " pdb=" N PRO A 112 " ideal model delta sigma weight residual 1.335 1.351 -0.017 1.28e-02 6.10e+03 1.72e+00 bond pdb=" CG1 ILE A 529 " pdb=" CD1 ILE A 529 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.57e+00 ... (remaining 24669 not shown) Histogram of bond angle deviations from ideal: 100.06 - 106.88: 514 106.88 - 113.69: 13871 113.69 - 120.51: 9589 120.51 - 127.32: 9340 127.32 - 134.13: 186 Bond angle restraints: 33500 Sorted by residual: angle pdb=" CA TYR C 300 " pdb=" CB TYR C 300 " pdb=" CG TYR C 300 " ideal model delta sigma weight residual 113.90 107.04 6.86 1.80e+00 3.09e-01 1.45e+01 angle pdb=" CA TYR D 300 " pdb=" CB TYR D 300 " pdb=" CG TYR D 300 " ideal model delta sigma weight residual 113.90 107.07 6.83 1.80e+00 3.09e-01 1.44e+01 angle pdb=" C THR C 87 " pdb=" N ILE C 88 " pdb=" CA ILE C 88 " ideal model delta sigma weight residual 122.59 119.98 2.61 7.20e-01 1.93e+00 1.32e+01 angle pdb=" C TYR A 187 " pdb=" CA TYR A 187 " pdb=" CB TYR A 187 " ideal model delta sigma weight residual 111.74 106.80 4.94 1.37e+00 5.33e-01 1.30e+01 angle pdb=" CA TYR A 300 " pdb=" CB TYR A 300 " pdb=" CG TYR A 300 " ideal model delta sigma weight residual 113.90 107.56 6.34 1.80e+00 3.09e-01 1.24e+01 ... (remaining 33495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 13105 17.67 - 35.33: 1150 35.33 - 53.00: 271 53.00 - 70.66: 76 70.66 - 88.33: 22 Dihedral angle restraints: 14624 sinusoidal: 5198 harmonic: 9426 Sorted by residual: dihedral pdb=" CA ASP A 161 " pdb=" C ASP A 161 " pdb=" N ASN A 162 " pdb=" CA ASN A 162 " ideal model delta harmonic sigma weight residual 180.00 -143.16 -36.84 0 5.00e+00 4.00e-02 5.43e+01 dihedral pdb=" CA PRO F 126 " pdb=" C PRO F 126 " pdb=" N LYS F 127 " pdb=" CA LYS F 127 " ideal model delta harmonic sigma weight residual -180.00 -149.66 -30.34 0 5.00e+00 4.00e-02 3.68e+01 dihedral pdb=" CA CYS F 111 " pdb=" C CYS F 111 " pdb=" N PRO F 112 " pdb=" CA PRO F 112 " ideal model delta harmonic sigma weight residual 180.00 -150.61 -29.39 0 5.00e+00 4.00e-02 3.46e+01 ... (remaining 14621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1934 0.033 - 0.066: 1326 0.066 - 0.099: 440 0.099 - 0.132: 156 0.132 - 0.165: 22 Chirality restraints: 3878 Sorted by residual: chirality pdb=" CB ILE B 500 " pdb=" CA ILE B 500 " pdb=" CG1 ILE B 500 " pdb=" CG2 ILE B 500 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.77e-01 chirality pdb=" CB ILE F 500 " pdb=" CA ILE F 500 " pdb=" CG1 ILE F 500 " pdb=" CG2 ILE F 500 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.63e-01 chirality pdb=" CB ILE C 500 " pdb=" CA ILE C 500 " pdb=" CG1 ILE C 500 " pdb=" CG2 ILE C 500 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.62e-01 ... (remaining 3875 not shown) Planarity restraints: 4288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 300 " 0.025 2.00e-02 2.50e+03 1.55e-02 4.78e+00 pdb=" CG TYR D 300 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR D 300 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR D 300 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR D 300 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR D 300 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR D 300 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 300 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 317 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO C 318 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 318 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 318 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 300 " -0.024 2.00e-02 2.50e+03 1.52e-02 4.65e+00 pdb=" CG TYR C 300 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR C 300 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR C 300 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR C 300 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 300 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR C 300 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 300 " -0.004 2.00e-02 2.50e+03 ... (remaining 4285 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 72 2.36 - 2.99: 12824 2.99 - 3.63: 35302 3.63 - 4.26: 60459 4.26 - 4.90: 98189 Nonbonded interactions: 206846 Sorted by model distance: nonbonded pdb=" O ASP E 475 " pdb="MN MN E 702 " model vdw 1.722 2.320 nonbonded pdb=" O ASP A 475 " pdb="MN MN A 702 " model vdw 1.722 2.320 nonbonded pdb=" O ASP C 475 " pdb="MN MN C 703 " model vdw 1.750 2.320 nonbonded pdb=" O ASP D 475 " pdb="MN MN D 703 " model vdw 1.752 2.320 nonbonded pdb=" NZ LYS A 390 " pdb="MN MN A 703 " model vdw 1.806 2.400 ... (remaining 206841 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' and (resid 75 through 81 or (resid 82 and (name N or name CA or name \ C or name O or name CB )) or resid 83 through 97 or (resid 98 and (name N or nam \ e CA or name C or name O or name CB )) or resid 99 or (resid 100 and (name N or \ name CA or name C or name O or name CB )) or resid 101 or (resid 102 and (name N \ or name CA or name C or name O or name CB )) or resid 103 through 110 or (resid \ 111 and (name N or name CA or name C or name O or name CB )) or resid 112 throu \ gh 113 or (resid 114 through 115 and (name N or name CA or name C or name O or n \ ame CB )) or resid 116 through 178 or (resid 179 and (name N or name CA or name \ C or name O or name CB )) or resid 180 through 182 or (resid 183 and (name N or \ name CA or name C or name O or name CB )) or resid 184 through 189 or (resid 190 \ and (name N or name CA or name C or name O or name CB )) or resid 191 through 1 \ 93 or (resid 194 and (name N or name CA or name C or name O or name CB )) or res \ id 195 through 210 or (resid 211 and (name N or name CA or name C or name O or n \ ame CB )) or resid 212 through 269 or (resid 270 through 272 and (name N or name \ CA or name C or name O or name CB )) or resid 273 through 379 or (resid 380 and \ (name N or name CA or name C or name O or name CB )) or resid 381 through 498 o \ r (resid 499 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 00 through 509 or (resid 510 and (name N or name CA or name C or name O or name \ CB )) or resid 511 through 523 or (resid 524 and (name N or name CA or name C or \ name O or name CB )) or resid 525 through 564 or (resid 565 and (name N or name \ CA or name C or name O or name CB )) or resid 566 through 599 or (resid 600 thr \ ough 601 and (name N or name CA or name C or name O or name CB )) or resid 602 t \ hrough 618 or (resid 619 and (name N or name CA or name C or name O or name CB ) \ ) or resid 701 through 703)) selection = (chain 'B' and (resid 75 through 81 or (resid 82 and (name N or name CA or name \ C or name O or name CB )) or resid 83 through 97 or (resid 98 and (name N or nam \ e CA or name C or name O or name CB )) or resid 99 or (resid 100 and (name N or \ name CA or name C or name O or name CB )) or resid 101 through 104 or (resid 105 \ and (name N or name CA or name C or name O or name CB )) or resid 106 through 1 \ 10 or (resid 111 and (name N or name CA or name C or name O or name CB )) or res \ id 112 through 126 or (resid 127 through 131 and (name N or name CA or name C or \ name O or name CB )) or (resid 132 through 170 and (name N or name CA or name C \ or name O or name CB )) or resid 171 through 178 or (resid 179 and (name N or n \ ame CA or name C or name O or name CB )) or resid 180 through 182 or (resid 183 \ and (name N or name CA or name C or name O or name CB )) or resid 184 through 18 \ 9 or (resid 190 and (name N or name CA or name C or name O or name CB )) or resi \ d 191 through 193 or (resid 194 and (name N or name CA or name C or name O or na \ me CB )) or resid 195 through 228 or (resid 229 and (name N or name CA or name C \ or name O or name CB )) or resid 230 or (resid 231 and (name N or name CA or na \ me C or name O or name CB )) or resid 232 through 239 or (resid 240 and (name N \ or name CA or name C or name O or name CB )) or resid 241 through 270 or (resid \ 271 through 272 and (name N or name CA or name C or name O or name CB )) or resi \ d 273 through 373 or (resid 374 and (name N or name CA or name C or name O or na \ me CB )) or resid 375 through 377 or (resid 378 through 380 and (name N or name \ CA or name C or name O or name CB )) or resid 381 through 523 or (resid 524 and \ (name N or name CA or name C or name O or name CB )) or resid 525 through 582 or \ (resid 583 and (name N or name CA or name C or name O or name CB )) or resid 58 \ 4 through 599 or (resid 600 through 601 and (name N or name CA or name C or name \ O or name CB )) or resid 602 through 618 or (resid 619 and (name N or name CA o \ r name C or name O or name CB )) or resid 701 through 703)) selection = (chain 'C' and (resid 75 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O or name CB )) or resid 103 through 113 or (resid 114 through 115 a \ nd (name N or name CA or name C or name O or name CB )) or resid 116 through 151 \ or (resid 152 through 170 and (name N or name CA or name C or name O or name CB \ )) or resid 171 through 178 or (resid 179 and (name N or name CA or name C or n \ ame O or name CB )) or resid 180 through 182 or (resid 183 and (name N or name C \ A or name C or name O or name CB )) or resid 184 through 189 or (resid 190 and ( \ name N or name CA or name C or name O or name CB )) or resid 191 through 193 or \ (resid 194 and (name N or name CA or name C or name O or name CB )) or resid 195 \ through 239 or (resid 240 and (name N or name CA or name C or name O or name CB \ )) or resid 241 through 266 or (resid 267 and (name N or name CA or name C or n \ ame O or name CB )) or resid 268 through 269 or (resid 270 through 272 and (name \ N or name CA or name C or name O or name CB )) or resid 273 through 377 or (res \ id 378 through 380 and (name N or name CA or name C or name O or name CB )) or r \ esid 381 through 498 or (resid 499 and (name N or name CA or name C or name O or \ name CB )) or resid 500 through 509 or (resid 510 and (name N or name CA or nam \ e C or name O or name CB )) or resid 511 through 564 or (resid 565 and (name N o \ r name CA or name C or name O or name CB )) or resid 566 through 582 or (resid 5 \ 83 and (name N or name CA or name C or name O or name CB )) or resid 584 through \ 599 or (resid 600 through 601 and (name N or name CA or name C or name O or nam \ e CB )) or resid 602 through 618 or (resid 619 and (name N or name CA or name C \ or name O or name CB )) or resid 701 through 703)) selection = (chain 'D' and (resid 75 through 81 or (resid 82 and (name N or name CA or name \ C or name O or name CB )) or resid 83 through 97 or (resid 98 and (name N or nam \ e CA or name C or name O or name CB )) or resid 99 or (resid 100 and (name N or \ name CA or name C or name O or name CB )) or resid 101 or (resid 102 and (name N \ or name CA or name C or name O or name CB )) or resid 103 through 108 or (resid \ 109 through 111 and (name N or name CA or name C or name O or name CB )) or res \ id 112 through 113 or (resid 114 through 115 and (name N or name CA or name C or \ name O or name CB )) or resid 116 through 152 or (resid 153 through 170 and (na \ me N or name CA or name C or name O or name CB )) or resid 171 through 178 or (r \ esid 179 and (name N or name CA or name C or name O or name CB )) or resid 180 t \ hrough 189 or (resid 190 and (name N or name CA or name C or name O or name CB ) \ ) or resid 191 through 193 or (resid 194 and (name N or name CA or name C or nam \ e O or name CB )) or resid 195 through 239 or (resid 240 and (name N or name CA \ or name C or name O or name CB )) or resid 241 through 266 or (resid 267 and (na \ me N or name CA or name C or name O or name CB )) or resid 268 through 269 or (r \ esid 270 through 272 and (name N or name CA or name C or name O or name CB )) or \ resid 273 through 373 or (resid 374 and (name N or name CA or name C or name O \ or name CB )) or resid 375 through 377 or (resid 378 through 380 and (name N or \ name CA or name C or name O or name CB )) or resid 381 through 509 or (resid 510 \ and (name N or name CA or name C or name O or name CB )) or resid 511 through 5 \ 64 or (resid 565 and (name N or name CA or name C or name O or name CB )) or res \ id 566 through 582 or (resid 583 and (name N or name CA or name C or name O or n \ ame CB )) or resid 584 through 619 or resid 701 through 703)) selection = (chain 'E' and (resid 75 through 97 or (resid 98 and (name N or name CA or name \ C or name O or name CB )) or resid 99 or (resid 100 and (name N or name CA or na \ me C or name O or name CB )) or resid 101 or (resid 102 and (name N or name CA o \ r name C or name O or name CB )) or resid 103 through 110 or (resid 111 and (nam \ e N or name CA or name C or name O or name CB )) or resid 112 through 113 or (re \ sid 114 through 115 and (name N or name CA or name C or name O or name CB )) or \ resid 116 through 128 or (resid 129 through 131 and (name N or name CA or name C \ or name O or name CB )) or resid 132 through 178 or (resid 179 and (name N or n \ ame CA or name C or name O or name CB )) or resid 180 through 182 or (resid 183 \ and (name N or name CA or name C or name O or name CB )) or resid 184 through 19 \ 3 or (resid 194 and (name N or name CA or name C or name O or name CB )) or resi \ d 195 through 210 or (resid 211 and (name N or name CA or name C or name O or na \ me CB )) or resid 212 through 266 or (resid 267 and (name N or name CA or name C \ or name O or name CB )) or resid 268 through 269 or (resid 270 through 272 and \ (name N or name CA or name C or name O or name CB )) or resid 273 through 373 or \ (resid 374 and (name N or name CA or name C or name O or name CB )) or resid 37 \ 5 through 377 or (resid 378 through 380 and (name N or name CA or name C or name \ O or name CB )) or resid 381 through 509 or (resid 510 and (name N or name CA o \ r name C or name O or name CB )) or resid 511 through 564 or (resid 565 and (nam \ e N or name CA or name C or name O or name CB )) or resid 566 through 618 or (re \ sid 619 and (name N or name CA or name C or name O or name CB )) or resid 701 th \ rough 703)) selection = (chain 'F' and (resid 75 through 81 or (resid 82 and (name N or name CA or name \ C or name O or name CB )) or resid 83 through 97 or (resid 98 and (name N or nam \ e CA or name C or name O or name CB )) or resid 99 or (resid 100 and (name N or \ name CA or name C or name O or name CB )) or resid 101 or (resid 102 and (name N \ or name CA or name C or name O or name CB )) or resid 103 through 110 or (resid \ 111 and (name N or name CA or name C or name O or name CB )) or resid 112 throu \ gh 113 or (resid 114 through 115 and (name N or name CA or name C or name O or n \ ame CB )) or resid 116 through 182 or (resid 183 and (name N or name CA or name \ C or name O or name CB )) or resid 184 through 189 or (resid 190 and (name N or \ name CA or name C or name O or name CB )) or resid 191 through 210 or (resid 211 \ and (name N or name CA or name C or name O or name CB )) or resid 212 through 2 \ 30 or (resid 231 and (name N or name CA or name C or name O or name CB )) or res \ id 232 through 270 or (resid 271 through 272 and (name N or name CA or name C or \ name O or name CB )) or resid 273 through 373 or (resid 374 and (name N or name \ CA or name C or name O or name CB )) or resid 375 through 377 or (resid 378 thr \ ough 380 and (name N or name CA or name C or name O or name CB )) or resid 381 t \ hrough 509 or (resid 510 and (name N or name CA or name C or name O or name CB ) \ ) or resid 511 through 599 or (resid 600 through 601 and (name N or name CA or n \ ame C or name O or name CB )) or resid 602 through 618 or (resid 619 and (name N \ or name CA or name C or name O or name CB )) or resid 701 through 703)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mn 12 7.51 5 S 89 5.16 5 C 15486 2.51 5 N 3986 2.21 5 O 4651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.520 Check model and map are aligned: 0.350 Process input model: 64.460 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.220 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:13.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 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 : 0.007 0.049 24674 Z= 0.460 Angle : 0.693 7.235 33500 Z= 0.387 Chirality : 0.048 0.165 3878 Planarity : 0.004 0.054 4288 Dihedral : 15.266 88.326 8612 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.22 % Favored : 89.75 % Rotamer Outliers : 4.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.12), residues: 3258 helix: -1.64 (0.13), residues: 1054 sheet: -1.33 (0.19), residues: 606 loop : -2.82 (0.12), residues: 1598 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 232 time to evaluate : 2.870 Fit side-chains outliers start: 99 outliers final: 64 residues processed: 320 average time/residue: 1.2593 time to fit residues: 471.0018 Evaluate side-chains 264 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 200 time to evaluate : 2.828 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 55 residues processed: 9 average time/residue: 0.5639 time to fit residues: 10.6694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 9.9990 chunk 245 optimal weight: 2.9990 chunk 136 optimal weight: 0.1980 chunk 83 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 253 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 154 optimal weight: 0.9990 chunk 189 optimal weight: 0.3980 chunk 294 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 HIS A 281 HIS A 307 GLN A 363 ASN A 436 ASN A 473 ASN A 527 ASN B 230 HIS B 307 GLN B 363 ASN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 ASN B 527 ASN B 584 ASN C 79 GLN C 230 HIS C 307 GLN C 363 ASN C 380 ASN C 527 ASN D 230 HIS D 307 GLN D 363 ASN D 380 ASN D 436 ASN D 473 ASN D 527 ASN E 93 HIS E 230 HIS E 307 GLN E 363 ASN E 473 ASN E 527 ASN F 230 HIS F 307 GLN F 363 ASN F 473 ASN F 527 ASN F 584 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 24674 Z= 0.133 Angle : 0.500 6.469 33500 Z= 0.274 Chirality : 0.042 0.137 3878 Planarity : 0.004 0.040 4288 Dihedral : 4.994 34.573 3468 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer Outliers : 3.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.96 (0.14), residues: 3258 helix: -0.29 (0.15), residues: 1055 sheet: -1.00 (0.20), residues: 674 loop : -2.18 (0.14), residues: 1529 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 219 time to evaluate : 3.145 Fit side-chains outliers start: 77 outliers final: 42 residues processed: 284 average time/residue: 1.1942 time to fit residues: 401.7334 Evaluate side-chains 242 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 200 time to evaluate : 2.923 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 36 residues processed: 6 average time/residue: 0.7669 time to fit residues: 9.9652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 chunk 200 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 294 optimal weight: 2.9990 chunk 318 optimal weight: 7.9990 chunk 262 optimal weight: 3.9990 chunk 292 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 236 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 ASN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 ASN E 93 HIS F 363 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.0870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.042 24674 Z= 0.402 Angle : 0.629 7.298 33500 Z= 0.340 Chirality : 0.047 0.186 3878 Planarity : 0.004 0.048 4288 Dihedral : 5.564 35.777 3468 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer Outliers : 4.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.03 % 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: -1.85 (0.14), residues: 3258 helix: -0.39 (0.15), residues: 1056 sheet: -0.60 (0.21), residues: 642 loop : -2.11 (0.14), residues: 1560 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 205 time to evaluate : 3.162 Fit side-chains outliers start: 100 outliers final: 65 residues processed: 284 average time/residue: 1.2130 time to fit residues: 409.4013 Evaluate side-chains 261 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 196 time to evaluate : 3.076 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 54 residues processed: 11 average time/residue: 0.3983 time to fit residues: 10.8369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 3.9990 chunk 221 optimal weight: 0.0970 chunk 152 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 197 optimal weight: 0.9990 chunk 295 optimal weight: 0.9990 chunk 313 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 280 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS A 123 ASN ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 524 GLN B 584 ASN F 584 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 24674 Z= 0.185 Angle : 0.511 6.350 33500 Z= 0.279 Chirality : 0.043 0.180 3878 Planarity : 0.003 0.043 4288 Dihedral : 4.979 33.437 3468 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer Outliers : 3.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.54 (0.14), residues: 3258 helix: -0.09 (0.15), residues: 1061 sheet: -0.69 (0.21), residues: 682 loop : -1.84 (0.14), residues: 1515 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 202 time to evaluate : 2.930 Fit side-chains outliers start: 88 outliers final: 60 residues processed: 276 average time/residue: 1.1645 time to fit residues: 381.5092 Evaluate side-chains 255 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 195 time to evaluate : 3.107 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 53 residues processed: 7 average time/residue: 0.5351 time to fit residues: 9.4984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 0.9990 chunk 177 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 233 optimal weight: 3.9990 chunk 129 optimal weight: 0.2980 chunk 267 optimal weight: 0.8980 chunk 216 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 159 optimal weight: 4.9990 chunk 281 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.0562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 524 GLN C 123 ASN ** D 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 ASN E 537 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 24674 Z= 0.144 Angle : 0.478 6.355 33500 Z= 0.260 Chirality : 0.042 0.199 3878 Planarity : 0.003 0.041 4288 Dihedral : 4.589 31.840 3468 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer Outliers : 3.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.20 (0.14), residues: 3258 helix: 0.24 (0.16), residues: 1045 sheet: -0.45 (0.21), residues: 676 loop : -1.68 (0.15), residues: 1537 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 201 time to evaluate : 2.900 Fit side-chains revert: symmetry clash outliers start: 84 outliers final: 61 residues processed: 268 average time/residue: 1.1623 time to fit residues: 371.9374 Evaluate side-chains 255 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 194 time to evaluate : 2.902 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 54 residues processed: 7 average time/residue: 0.6796 time to fit residues: 10.0249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 3.9990 chunk 282 optimal weight: 10.0000 chunk 61 optimal weight: 50.0000 chunk 183 optimal weight: 9.9990 chunk 77 optimal weight: 0.6980 chunk 313 optimal weight: 0.6980 chunk 260 optimal weight: 0.9990 chunk 145 optimal weight: 8.9990 chunk 26 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 HIS B 363 ASN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 HIS F 363 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 24674 Z= 0.216 Angle : 0.516 6.335 33500 Z= 0.279 Chirality : 0.043 0.174 3878 Planarity : 0.003 0.043 4288 Dihedral : 4.786 31.473 3468 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer Outliers : 3.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.05 (0.14), residues: 3258 helix: 0.34 (0.16), residues: 1018 sheet: -0.44 (0.21), residues: 680 loop : -1.51 (0.15), residues: 1560 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 202 time to evaluate : 3.008 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 63 residues processed: 272 average time/residue: 1.1845 time to fit residues: 383.1087 Evaluate side-chains 255 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 192 time to evaluate : 3.098 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 58 residues processed: 5 average time/residue: 0.9079 time to fit residues: 9.6785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 178 optimal weight: 5.9990 chunk 228 optimal weight: 9.9990 chunk 177 optimal weight: 9.9990 chunk 263 optimal weight: 0.9990 chunk 175 optimal weight: 6.9990 chunk 312 optimal weight: 7.9990 chunk 195 optimal weight: 7.9990 chunk 190 optimal weight: 8.9990 chunk 144 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 HIS E 252 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.047 24674 Z= 0.466 Angle : 0.657 7.113 33500 Z= 0.353 Chirality : 0.049 0.228 3878 Planarity : 0.004 0.050 4288 Dihedral : 5.583 33.314 3468 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer Outliers : 3.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.03 % 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: -1.42 (0.14), residues: 3258 helix: -0.15 (0.15), residues: 1053 sheet: -0.38 (0.21), residues: 658 loop : -1.74 (0.15), residues: 1547 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 206 time to evaluate : 2.850 Fit side-chains revert: symmetry clash outliers start: 85 outliers final: 66 residues processed: 281 average time/residue: 1.1796 time to fit residues: 398.1753 Evaluate side-chains 267 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 201 time to evaluate : 2.996 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 60 residues processed: 6 average time/residue: 0.8442 time to fit residues: 10.8414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 186 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 61 optimal weight: 0.2980 chunk 60 optimal weight: 0.7980 chunk 198 optimal weight: 0.9980 chunk 212 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 245 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 ASN F 584 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 24674 Z= 0.147 Angle : 0.486 6.903 33500 Z= 0.265 Chirality : 0.042 0.209 3878 Planarity : 0.003 0.042 4288 Dihedral : 4.687 28.932 3468 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer Outliers : 3.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.14), residues: 3258 helix: 0.36 (0.16), residues: 1015 sheet: -0.36 (0.21), residues: 678 loop : -1.39 (0.15), residues: 1565 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 200 time to evaluate : 3.174 Fit side-chains revert: symmetry clash outliers start: 80 outliers final: 61 residues processed: 270 average time/residue: 1.1882 time to fit residues: 383.4519 Evaluate side-chains 258 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 197 time to evaluate : 2.965 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 55 residues processed: 6 average time/residue: 0.5174 time to fit residues: 8.2011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 6.9990 chunk 299 optimal weight: 9.9990 chunk 272 optimal weight: 2.9990 chunk 291 optimal weight: 0.0980 chunk 175 optimal weight: 0.0040 chunk 126 optimal weight: 5.9990 chunk 228 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 262 optimal weight: 0.0770 chunk 275 optimal weight: 30.0000 chunk 289 optimal weight: 10.0000 overall best weight: 1.2354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 ASN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 363 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 24674 Z= 0.159 Angle : 0.493 8.966 33500 Z= 0.267 Chirality : 0.042 0.216 3878 Planarity : 0.003 0.041 4288 Dihedral : 4.571 28.148 3468 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer Outliers : 2.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.15), residues: 3258 helix: 0.49 (0.16), residues: 1017 sheet: -0.31 (0.21), residues: 683 loop : -1.34 (0.15), residues: 1558 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 195 time to evaluate : 3.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 59 residues processed: 254 average time/residue: 1.1842 time to fit residues: 363.1947 Evaluate side-chains 247 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 188 time to evaluate : 2.743 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 56 residues processed: 3 average time/residue: 0.2553 time to fit residues: 5.2138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 5.9990 chunk 307 optimal weight: 7.9990 chunk 187 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 322 optimal weight: 2.9990 chunk 297 optimal weight: 2.9990 chunk 257 optimal weight: 8.9990 chunk 26 optimal weight: 0.3980 chunk 198 optimal weight: 0.5980 chunk 157 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 524 GLN D 330 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 24674 Z= 0.138 Angle : 0.472 8.950 33500 Z= 0.256 Chirality : 0.042 0.194 3878 Planarity : 0.003 0.040 4288 Dihedral : 4.342 27.407 3468 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer Outliers : 2.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.15), residues: 3258 helix: 0.64 (0.16), residues: 1016 sheet: -0.21 (0.21), residues: 679 loop : -1.25 (0.15), residues: 1563 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 192 time to evaluate : 3.152 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 56 residues processed: 251 average time/residue: 1.1905 time to fit residues: 356.5239 Evaluate side-chains 246 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 190 time to evaluate : 2.842 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 55 residues processed: 1 average time/residue: 0.2815 time to fit residues: 4.4474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 7.9990 chunk 273 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 237 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 257 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 264 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 524 GLN E 93 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.138017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.106501 restraints weight = 28010.124| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.65 r_work: 0.2933 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 24674 Z= 0.355 Angle : 0.598 10.359 33500 Z= 0.321 Chirality : 0.046 0.224 3878 Planarity : 0.004 0.046 4288 Dihedral : 5.121 29.222 3468 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer Outliers : 2.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.14), residues: 3258 helix: 0.26 (0.16), residues: 1036 sheet: -0.40 (0.21), residues: 693 loop : -1.51 (0.15), residues: 1529 =============================================================================== Job complete usr+sys time: 7104.39 seconds wall clock time: 128 minutes 55.48 seconds (7735.48 seconds total)