Starting phenix.real_space_refine on Mon Mar 18 15:27:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2r_23138/03_2024/7l2r_23138_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2r_23138/03_2024/7l2r_23138.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2r_23138/03_2024/7l2r_23138_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2r_23138/03_2024/7l2r_23138_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2r_23138/03_2024/7l2r_23138_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2r_23138/03_2024/7l2r_23138.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2r_23138/03_2024/7l2r_23138.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2r_23138/03_2024/7l2r_23138_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2r_23138/03_2024/7l2r_23138_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 138 5.16 5 Na 1 4.78 5 C 13895 2.51 5 N 3453 2.21 5 O 3882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 557": "NH1" <-> "NH2" Residue "A GLU 600": "OE1" <-> "OE2" Residue "B ARG 428": "NH1" <-> "NH2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B GLU 570": "OE1" <-> "OE2" Residue "C GLU 210": "OE1" <-> "OE2" Residue "C ARG 428": "NH1" <-> "NH2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 557": "NH1" <-> "NH2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "D ARG 534": "NH1" <-> "NH2" Residue "D ARG 557": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21377 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4974 Classifications: {'peptide': 615} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 598} Chain: "F" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 591 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "E" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 591 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "B" Number of atoms: 4963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4963 Classifications: {'peptide': 614} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 597} Chain: "C" Number of atoms: 5002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 618, 5002 Classifications: {'peptide': 618} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 601} Chain: "D" Number of atoms: 4963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4963 Classifications: {'peptide': 614} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 597} Chain: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 73 Unusual residues: {' NA': 1, '65I': 1, 'XJ7': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'65I': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'XJ7': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'65I': 1, 'XJ7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'65I': 1, 'XJ7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 11.22, per 1000 atoms: 0.52 Number of scatterers: 21377 At special positions: 0 Unit cell: (136.657, 139.203, 133.262, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 138 16.00 P 8 15.00 Na 1 11.00 O 3882 8.00 N 3453 7.00 C 13895 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS F 2 " - pdb=" SG CYS F 16 " distance=2.03 Simple disulfide: pdb=" SG CYS F 9 " - pdb=" SG CYS F 23 " distance=2.04 Simple disulfide: pdb=" SG CYS F 15 " - pdb=" SG CYS F 31 " distance=2.03 Simple disulfide: pdb=" SG CYS F 44 " - pdb=" SG CYS F 58 " distance=2.03 Simple disulfide: pdb=" SG CYS F 51 " - pdb=" SG CYS F 63 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 71 " distance=2.02 Simple disulfide: pdb=" SG CYS E 2 " - pdb=" SG CYS E 16 " distance=2.04 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 23 " distance=2.04 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 31 " distance=2.03 Simple disulfide: pdb=" SG CYS E 44 " - pdb=" SG CYS E 58 " distance=2.03 Simple disulfide: pdb=" SG CYS E 51 " - pdb=" SG CYS E 63 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 71 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.91 Conformation dependent library (CDL) restraints added in 3.6 seconds 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4950 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 115 helices and 5 sheets defined 53.0% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.21 Creating SS restraints... Processing helix chain 'A' and resid 115 through 122 Processing helix chain 'A' and resid 127 through 139 removed outlier: 3.780A pdb=" N GLU A 130 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER A 131 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU A 133 " --> pdb=" O GLU A 130 " (cutoff:3.500A) Proline residue: A 134 - end of helix removed outlier: 3.599A pdb=" N GLN A 137 " --> pdb=" O PRO A 134 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A 139 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 163 Processing helix chain 'A' and resid 172 through 183 Processing helix chain 'A' and resid 197 through 199 No H-bonds generated for 'chain 'A' and resid 197 through 199' Processing helix chain 'A' and resid 204 through 210 Processing helix chain 'A' and resid 214 through 222 Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 251 through 257 Processing helix chain 'A' and resid 261 through 269 Processing helix chain 'A' and resid 287 through 293 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 346 through 354 removed outlier: 4.382A pdb=" N GLN A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 416 through 428 removed outlier: 4.092A pdb=" N ARG A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 453 Processing helix chain 'A' and resid 470 through 499 Processing helix chain 'A' and resid 505 through 508 No H-bonds generated for 'chain 'A' and resid 505 through 508' Processing helix chain 'A' and resid 511 through 531 Processing helix chain 'A' and resid 536 through 556 removed outlier: 4.194A pdb=" N MET A 547 " --> pdb=" O SER A 544 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASN A 551 " --> pdb=" O GLY A 548 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 553 " --> pdb=" O THR A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 575 Processing helix chain 'A' and resid 577 through 598 removed outlier: 4.402A pdb=" N PHE A 582 " --> pdb=" O CYS A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 641 removed outlier: 4.001A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 670 Processing helix chain 'A' and resid 674 through 688 removed outlier: 3.880A pdb=" N ASN A 687 " --> pdb=" O GLY A 683 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS A 688 " --> pdb=" O GLU A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 709 removed outlier: 4.301A pdb=" N LYS A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN A 695 " --> pdb=" O GLN A 691 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 20 No H-bonds generated for 'chain 'E' and resid 18 through 20' Processing helix chain 'B' and resid 116 through 123 Processing helix chain 'B' and resid 126 through 128 No H-bonds generated for 'chain 'B' and resid 126 through 128' Processing helix chain 'B' and resid 132 through 135 No H-bonds generated for 'chain 'B' and resid 132 through 135' Processing helix chain 'B' and resid 157 through 163 Processing helix chain 'B' and resid 171 through 183 Processing helix chain 'B' and resid 187 through 190 No H-bonds generated for 'chain 'B' and resid 187 through 190' Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 251 through 257 Processing helix chain 'B' and resid 261 through 269 Processing helix chain 'B' and resid 287 through 293 Processing helix chain 'B' and resid 299 through 319 Processing helix chain 'B' and resid 325 through 327 No H-bonds generated for 'chain 'B' and resid 325 through 327' Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 346 through 354 removed outlier: 4.028A pdb=" N GLN B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 411 through 414 Processing helix chain 'B' and resid 416 through 428 removed outlier: 3.982A pdb=" N ARG B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 453 Processing helix chain 'B' and resid 469 through 499 Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 511 through 531 Processing helix chain 'B' and resid 536 through 556 removed outlier: 4.245A pdb=" N VAL B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA B 546 " --> pdb=" O PHE B 543 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TRP B 549 " --> pdb=" O ALA B 546 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN B 551 " --> pdb=" O GLY B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 575 Processing helix chain 'B' and resid 577 through 598 removed outlier: 3.741A pdb=" N PHE B 582 " --> pdb=" O CYS B 578 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 641 removed outlier: 4.168A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 670 Processing helix chain 'B' and resid 673 through 688 removed outlier: 3.635A pdb=" N ILE B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 711 removed outlier: 4.236A pdb=" N LYS B 694 " --> pdb=" O ALA B 690 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN B 695 " --> pdb=" O GLN B 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 123 Processing helix chain 'C' and resid 126 through 139 removed outlier: 3.587A pdb=" N GLU C 130 " --> pdb=" O GLN C 127 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER C 131 " --> pdb=" O GLU C 128 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LEU C 133 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Proline residue: C 134 - end of helix Processing helix chain 'C' and resid 157 through 163 Processing helix chain 'C' and resid 172 through 183 Processing helix chain 'C' and resid 187 through 190 No H-bonds generated for 'chain 'C' and resid 187 through 190' Processing helix chain 'C' and resid 204 through 210 Processing helix chain 'C' and resid 214 through 222 Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 251 through 257 Processing helix chain 'C' and resid 261 through 269 Processing helix chain 'C' and resid 287 through 293 Processing helix chain 'C' and resid 299 through 319 Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'C' and resid 346 through 354 removed outlier: 4.136A pdb=" N GLN C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 395 through 400 Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 416 through 428 removed outlier: 3.980A pdb=" N ARG C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 453 Processing helix chain 'C' and resid 469 through 499 Processing helix chain 'C' and resid 511 through 531 Processing helix chain 'C' and resid 535 through 556 removed outlier: 3.681A pdb=" N SER C 540 " --> pdb=" O TYR C 537 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE C 543 " --> pdb=" O SER C 540 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET C 547 " --> pdb=" O SER C 544 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TRP C 549 " --> pdb=" O ALA C 546 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET C 552 " --> pdb=" O TRP C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 575 Processing helix chain 'C' and resid 577 through 598 removed outlier: 3.958A pdb=" N PHE C 582 " --> pdb=" O CYS C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 641 removed outlier: 4.184A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 659 through 670 Processing helix chain 'C' and resid 673 through 688 removed outlier: 3.556A pdb=" N ILE C 679 " --> pdb=" O LEU C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 711 removed outlier: 4.333A pdb=" N LYS C 694 " --> pdb=" O ALA C 690 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN C 695 " --> pdb=" O GLN C 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 123 Processing helix chain 'D' and resid 132 through 139 Processing helix chain 'D' and resid 157 through 163 Processing helix chain 'D' and resid 172 through 183 Processing helix chain 'D' and resid 204 through 210 Processing helix chain 'D' and resid 214 through 222 Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 251 through 257 Processing helix chain 'D' and resid 261 through 269 Processing helix chain 'D' and resid 287 through 293 Processing helix chain 'D' and resid 299 through 319 Processing helix chain 'D' and resid 325 through 327 No H-bonds generated for 'chain 'D' and resid 325 through 327' Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 346 through 354 removed outlier: 3.943A pdb=" N GLN D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 365 No H-bonds generated for 'chain 'D' and resid 363 through 365' Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 412 through 414 No H-bonds generated for 'chain 'D' and resid 412 through 414' Processing helix chain 'D' and resid 416 through 428 removed outlier: 3.866A pdb=" N ARG D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 453 Processing helix chain 'D' and resid 469 through 499 Processing helix chain 'D' and resid 511 through 531 Processing helix chain 'D' and resid 536 through 556 removed outlier: 3.991A pdb=" N SER D 540 " --> pdb=" O TYR D 537 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TRP D 549 " --> pdb=" O ALA D 546 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN D 551 " --> pdb=" O GLY D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 598 removed outlier: 4.068A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG D 579 " --> pdb=" O ARG D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 641 removed outlier: 3.868A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 659 through 670 Processing helix chain 'D' and resid 673 through 688 removed outlier: 3.745A pdb=" N ILE D 679 " --> pdb=" O LEU D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 710 removed outlier: 4.224A pdb=" N LYS D 694 " --> pdb=" O ALA D 690 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN D 695 " --> pdb=" O GLN D 691 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 741 through 747 removed outlier: 3.925A pdb=" N TRP A 372 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ASP A 383 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LYS A 368 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'F' and resid 21 through 23 Processing sheet with id= C, first strand: chain 'B' and resid 741 through 747 removed outlier: 3.615A pdb=" N TRP B 372 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ASP B 383 " --> pdb=" O LYS B 368 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LYS B 368 " --> pdb=" O ASP B 383 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 741 through 747 removed outlier: 3.640A pdb=" N TRP C 372 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ASP C 383 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LYS C 368 " --> pdb=" O ASP C 383 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 741 through 747 removed outlier: 3.729A pdb=" N TRP D 372 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ASP D 383 " --> pdb=" O LYS D 368 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LYS D 368 " --> pdb=" O ASP D 383 " (cutoff:3.500A) 911 hydrogen bonds defined for protein. 2538 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.56 Time building geometry restraints manager: 8.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3355 1.30 - 1.43: 6073 1.43 - 1.56: 12199 1.56 - 1.70: 16 1.70 - 1.83: 208 Bond restraints: 21851 Sorted by residual: bond pdb=" C ARG A 500 " pdb=" O ARG A 500 " ideal model delta sigma weight residual 1.235 1.261 -0.026 4.70e-03 4.53e+04 2.97e+01 bond pdb=" C11 65I D 802 " pdb=" O6 65I D 802 " ideal model delta sigma weight residual 1.331 1.401 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C11 65I A 802 " pdb=" O6 65I A 802 " ideal model delta sigma weight residual 1.331 1.401 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C11 65I F 901 " pdb=" O6 65I F 901 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C11 65I C 901 " pdb=" O6 65I C 901 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 21846 not shown) Histogram of bond angle deviations from ideal: 97.45 - 104.76: 286 104.76 - 112.08: 10403 112.08 - 119.40: 7870 119.40 - 126.71: 10731 126.71 - 134.03: 238 Bond angle restraints: 29528 Sorted by residual: angle pdb=" N SER D 722 " pdb=" CA SER D 722 " pdb=" C SER D 722 " ideal model delta sigma weight residual 112.94 124.35 -11.41 1.41e+00 5.03e-01 6.55e+01 angle pdb=" O3 65I A 802 " pdb=" P 65I A 802 " pdb=" O4 65I A 802 " ideal model delta sigma weight residual 122.02 100.69 21.33 3.00e+00 1.11e-01 5.06e+01 angle pdb=" O3 65I F 901 " pdb=" P 65I F 901 " pdb=" O4 65I F 901 " ideal model delta sigma weight residual 122.02 100.77 21.25 3.00e+00 1.11e-01 5.02e+01 angle pdb=" O3 65I D 802 " pdb=" P 65I D 802 " pdb=" O4 65I D 802 " ideal model delta sigma weight residual 122.02 100.83 21.19 3.00e+00 1.11e-01 4.99e+01 angle pdb=" O3 65I C 901 " pdb=" P 65I C 901 " pdb=" O4 65I C 901 " ideal model delta sigma weight residual 122.02 101.24 20.78 3.00e+00 1.11e-01 4.80e+01 ... (remaining 29523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.75: 12810 29.75 - 59.49: 227 59.49 - 89.24: 38 89.24 - 118.98: 12 118.98 - 148.73: 5 Dihedral angle restraints: 13092 sinusoidal: 5402 harmonic: 7690 Sorted by residual: dihedral pdb=" CA VAL B 415 " pdb=" C VAL B 415 " pdb=" N GLU B 416 " pdb=" CA GLU B 416 " ideal model delta harmonic sigma weight residual -180.00 -150.69 -29.31 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA VAL C 415 " pdb=" C VAL C 415 " pdb=" N GLU C 416 " pdb=" CA GLU C 416 " ideal model delta harmonic sigma weight residual 180.00 -151.52 -28.48 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA VAL A 415 " pdb=" C VAL A 415 " pdb=" N GLU A 416 " pdb=" CA GLU A 416 " ideal model delta harmonic sigma weight residual -180.00 -151.83 -28.17 0 5.00e+00 4.00e-02 3.17e+01 ... (remaining 13089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.005: 3302 1.005 - 2.010: 0 2.010 - 3.015: 0 3.015 - 4.020: 0 4.020 - 5.025: 8 Chirality restraints: 3310 Sorted by residual: chirality pdb=" C3 XJ7 B 801 " pdb=" C2 XJ7 B 801 " pdb=" C24 XJ7 B 801 " pdb=" O3 XJ7 B 801 " both_signs ideal model delta sigma weight residual False -2.50 2.52 -5.03 2.00e-01 2.50e+01 6.31e+02 chirality pdb=" C3 XJ7 D 801 " pdb=" C2 XJ7 D 801 " pdb=" C24 XJ7 D 801 " pdb=" O3 XJ7 D 801 " both_signs ideal model delta sigma weight residual False -2.50 2.51 -5.01 2.00e-01 2.50e+01 6.29e+02 chirality pdb=" C3 XJ7 A 801 " pdb=" C2 XJ7 A 801 " pdb=" C24 XJ7 A 801 " pdb=" O3 XJ7 A 801 " both_signs ideal model delta sigma weight residual False -2.50 2.51 -5.01 2.00e-01 2.50e+01 6.28e+02 ... (remaining 3307 not shown) Planarity restraints: 3665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 540 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.09e+00 pdb=" C SER A 540 " -0.049 2.00e-02 2.50e+03 pdb=" O SER A 540 " 0.019 2.00e-02 2.50e+03 pdb=" N MET A 541 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 539 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.72e+00 pdb=" C ALA A 539 " 0.045 2.00e-02 2.50e+03 pdb=" O ALA A 539 " -0.017 2.00e-02 2.50e+03 pdb=" N SER A 540 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 544 " 0.012 2.00e-02 2.50e+03 2.36e-02 5.56e+00 pdb=" C SER D 544 " -0.041 2.00e-02 2.50e+03 pdb=" O SER D 544 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU D 545 " 0.014 2.00e-02 2.50e+03 ... (remaining 3662 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 240 2.67 - 3.23: 20725 3.23 - 3.78: 30455 3.78 - 4.34: 41458 4.34 - 4.90: 70308 Nonbonded interactions: 163186 Sorted by model distance: nonbonded pdb=" OG SER C 722 " pdb=" O CYS C 741 " model vdw 2.112 2.440 nonbonded pdb=" OG SER B 722 " pdb=" O CYS B 741 " model vdw 2.159 2.440 nonbonded pdb=" O GLY B 485 " pdb=" OG SER B 520 " model vdw 2.339 2.440 nonbonded pdb=" OG SER C 185 " pdb=" OE1 GLN C 188 " model vdw 2.368 2.440 nonbonded pdb=" N GLU B 536 " pdb=" OE1 GLU B 536 " model vdw 2.374 2.520 ... (remaining 163181 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 115 through 751) selection = (chain 'B' and resid 115 through 751) selection = (chain 'C' and resid 115 through 751) selection = (chain 'D' and resid 115 through 751) } ncs_group { reference = chain 'E' selection = (chain 'F' and resid 1 through 75) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 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: 8.030 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 53.010 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 21851 Z= 0.504 Angle : 0.918 21.334 29528 Z= 0.478 Chirality : 0.250 5.025 3310 Planarity : 0.005 0.044 3665 Dihedral : 13.324 148.725 8106 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.62 % Favored : 93.31 % Rotamer: Outliers : 0.35 % Allowed : 1.21 % Favored : 98.44 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 5.26 % 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: -0.23 (0.16), residues: 2599 helix: 0.97 (0.13), residues: 1467 sheet: -1.27 (0.51), residues: 80 loop : -1.71 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 740 HIS 0.004 0.001 HIS A 364 PHE 0.026 0.003 PHE D 730 TYR 0.018 0.002 TYR A 453 ARG 0.005 0.001 ARG C 721 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 594 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8439 (t70) cc_final: 0.8124 (m-30) REVERT: A 221 VAL cc_start: 0.8552 (t) cc_final: 0.8333 (m) REVERT: A 576 ASP cc_start: 0.8536 (m-30) cc_final: 0.8255 (m-30) REVERT: F 5 GLU cc_start: 0.7368 (tt0) cc_final: 0.7119 (tt0) REVERT: F 20 ASN cc_start: 0.8395 (m-40) cc_final: 0.8045 (m110) REVERT: B 223 ASN cc_start: 0.8243 (m110) cc_final: 0.7809 (m110) REVERT: B 304 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.8368 (t80) REVERT: B 306 THR cc_start: 0.9326 (m) cc_final: 0.9007 (p) REVERT: B 646 ASP cc_start: 0.7874 (t70) cc_final: 0.7371 (t0) REVERT: C 210 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8503 (tm-30) REVERT: C 213 ASN cc_start: 0.8339 (t0) cc_final: 0.7828 (t0) REVERT: C 221 VAL cc_start: 0.8836 (t) cc_final: 0.8594 (m) REVERT: C 325 LEU cc_start: 0.9426 (mt) cc_final: 0.9224 (mt) REVERT: C 389 THR cc_start: 0.8914 (t) cc_final: 0.8440 (p) REVERT: C 570 GLU cc_start: 0.7547 (tt0) cc_final: 0.7255 (tt0) REVERT: C 646 ASP cc_start: 0.8120 (t0) cc_final: 0.7885 (t0) REVERT: D 213 ASN cc_start: 0.8926 (t0) cc_final: 0.8168 (t0) REVERT: D 392 LYS cc_start: 0.8622 (tptt) cc_final: 0.8391 (tptm) REVERT: D 509 ASP cc_start: 0.8609 (t0) cc_final: 0.8346 (m-30) REVERT: D 510 SER cc_start: 0.9107 (m) cc_final: 0.8902 (p) REVERT: D 550 THR cc_start: 0.9498 (m) cc_final: 0.9165 (p) REVERT: D 646 ASP cc_start: 0.7588 (t0) cc_final: 0.7288 (t0) REVERT: D 716 MET cc_start: 0.5346 (ptt) cc_final: 0.4366 (mmm) outliers start: 8 outliers final: 5 residues processed: 599 average time/residue: 0.3692 time to fit residues: 324.3039 Evaluate side-chains 415 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 408 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 21 PHE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 390 CYS Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 390 CYS Chi-restraints excluded: chain D residue 720 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 217 optimal weight: 6.9990 chunk 195 optimal weight: 0.1980 chunk 108 optimal weight: 0.9980 chunk 66 optimal weight: 20.0000 chunk 131 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 202 optimal weight: 20.0000 chunk 78 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 150 optimal weight: 7.9990 chunk 234 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN B 498 GLN C 223 ASN ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN D 223 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21851 Z= 0.172 Angle : 0.571 11.480 29528 Z= 0.298 Chirality : 0.042 0.317 3310 Planarity : 0.004 0.043 3665 Dihedral : 11.878 130.360 3111 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.81 % Favored : 94.07 % Rotamer: Outliers : 1.90 % Allowed : 6.79 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.49 (0.17), residues: 2599 helix: 1.70 (0.13), residues: 1452 sheet: -0.60 (0.53), residues: 80 loop : -1.63 (0.19), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 740 HIS 0.003 0.001 HIS F 59 PHE 0.020 0.001 PHE A 659 TYR 0.027 0.001 TYR B 199 ARG 0.006 0.000 ARG C 331 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 447 time to evaluate : 2.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8418 (t70) cc_final: 0.8143 (m-30) REVERT: A 445 MET cc_start: 0.9239 (mmm) cc_final: 0.8997 (mmt) REVERT: A 576 ASP cc_start: 0.8514 (m-30) cc_final: 0.8210 (m-30) REVERT: F 5 GLU cc_start: 0.7114 (tt0) cc_final: 0.6901 (tt0) REVERT: F 46 LYS cc_start: 0.8169 (mtmm) cc_final: 0.7690 (mtmm) REVERT: B 213 ASN cc_start: 0.8584 (t0) cc_final: 0.7994 (t0) REVERT: B 223 ASN cc_start: 0.8212 (m110) cc_final: 0.7758 (m110) REVERT: B 306 THR cc_start: 0.9334 (m) cc_final: 0.9061 (p) REVERT: B 646 ASP cc_start: 0.7755 (t70) cc_final: 0.7302 (t0) REVERT: C 219 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8832 (tp) REVERT: C 389 THR cc_start: 0.8881 (t) cc_final: 0.8444 (p) REVERT: D 213 ASN cc_start: 0.8822 (t0) cc_final: 0.8374 (t0) REVERT: D 216 LEU cc_start: 0.9315 (mp) cc_final: 0.8781 (mp) REVERT: D 466 LYS cc_start: 0.7956 (tptp) cc_final: 0.7599 (mtpp) REVERT: D 550 THR cc_start: 0.9403 (m) cc_final: 0.9105 (p) REVERT: D 646 ASP cc_start: 0.7518 (t0) cc_final: 0.7235 (t0) REVERT: D 716 MET cc_start: 0.4898 (ptt) cc_final: 0.4166 (mmm) outliers start: 44 outliers final: 30 residues processed: 471 average time/residue: 0.3351 time to fit residues: 239.2838 Evaluate side-chains 425 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 394 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain B residue 720 PHE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 733 ASP Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 390 CYS Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 649 PHE Chi-restraints excluded: chain D residue 720 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 130 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 234 optimal weight: 0.9980 chunk 253 optimal weight: 3.9990 chunk 209 optimal weight: 0.2980 chunk 232 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 188 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS B 498 GLN C 393 ASN D 191 ASN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21851 Z= 0.181 Angle : 0.535 14.021 29528 Z= 0.280 Chirality : 0.039 0.233 3310 Planarity : 0.004 0.045 3665 Dihedral : 10.704 128.240 3105 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.35 % Favored : 93.61 % Rotamer: Outliers : 2.33 % Allowed : 8.99 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.72 (0.17), residues: 2599 helix: 1.89 (0.14), residues: 1465 sheet: -0.34 (0.53), residues: 80 loop : -1.60 (0.19), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 740 HIS 0.002 0.001 HIS A 166 PHE 0.017 0.001 PHE C 582 TYR 0.016 0.001 TYR B 199 ARG 0.005 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 416 time to evaluate : 2.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8371 (t70) cc_final: 0.8066 (m-30) REVERT: A 220 LEU cc_start: 0.9298 (mm) cc_final: 0.8973 (mm) REVERT: A 576 ASP cc_start: 0.8481 (m-30) cc_final: 0.8171 (m-30) REVERT: F 5 GLU cc_start: 0.6822 (tt0) cc_final: 0.6402 (tt0) REVERT: B 213 ASN cc_start: 0.8577 (t0) cc_final: 0.7874 (t0) REVERT: B 223 ASN cc_start: 0.8171 (m110) cc_final: 0.7725 (m110) REVERT: B 306 THR cc_start: 0.9351 (m) cc_final: 0.9148 (p) REVERT: B 524 LEU cc_start: 0.8906 (mt) cc_final: 0.8703 (mt) REVERT: B 646 ASP cc_start: 0.7846 (t70) cc_final: 0.7350 (t0) REVERT: C 389 THR cc_start: 0.8909 (t) cc_final: 0.8514 (p) REVERT: D 213 ASN cc_start: 0.8798 (t0) cc_final: 0.8558 (t0) REVERT: D 536 GLU cc_start: 0.8501 (mp0) cc_final: 0.8085 (mp0) REVERT: D 646 ASP cc_start: 0.7532 (t0) cc_final: 0.7222 (t0) REVERT: D 651 GLU cc_start: 0.7886 (tp30) cc_final: 0.7640 (tp30) REVERT: D 716 MET cc_start: 0.4817 (ptt) cc_final: 0.4082 (mmm) REVERT: D 730 PHE cc_start: 0.8212 (m-80) cc_final: 0.7768 (m-80) outliers start: 54 outliers final: 40 residues processed: 446 average time/residue: 0.3419 time to fit residues: 231.6679 Evaluate side-chains 431 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 391 time to evaluate : 2.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain B residue 720 PHE Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 390 CYS Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 733 ASP Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 649 PHE Chi-restraints excluded: chain D residue 720 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 231 optimal weight: 0.6980 chunk 176 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 chunk 157 optimal weight: 0.3980 chunk 235 optimal weight: 5.9990 chunk 249 optimal weight: 2.9990 chunk 123 optimal weight: 0.0000 chunk 223 optimal weight: 8.9990 chunk 67 optimal weight: 20.0000 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 498 GLN D 191 ASN D 378 HIS ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 21851 Z= 0.156 Angle : 0.509 11.146 29528 Z= 0.268 Chirality : 0.039 0.189 3310 Planarity : 0.003 0.046 3665 Dihedral : 10.127 127.184 3104 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.42 % Allowed : 9.73 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.17), residues: 2599 helix: 2.08 (0.14), residues: 1460 sheet: -0.09 (0.54), residues: 80 loop : -1.51 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 740 HIS 0.003 0.000 HIS A 166 PHE 0.015 0.001 PHE C 582 TYR 0.014 0.001 TYR B 199 ARG 0.005 0.000 ARG B 242 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 417 time to evaluate : 2.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8377 (t70) cc_final: 0.8065 (m-30) REVERT: A 220 LEU cc_start: 0.9307 (mm) cc_final: 0.8992 (mm) REVERT: A 576 ASP cc_start: 0.8467 (m-30) cc_final: 0.8134 (m-30) REVERT: A 584 TYR cc_start: 0.9013 (t80) cc_final: 0.8717 (t80) REVERT: A 710 LYS cc_start: 0.8833 (ttmt) cc_final: 0.8525 (tppt) REVERT: F 5 GLU cc_start: 0.6514 (tt0) cc_final: 0.6302 (tt0) REVERT: B 213 ASN cc_start: 0.8525 (t0) cc_final: 0.8115 (t0) REVERT: B 223 ASN cc_start: 0.8244 (m110) cc_final: 0.7804 (m110) REVERT: B 306 THR cc_start: 0.9353 (m) cc_final: 0.9121 (p) REVERT: B 327 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8077 (mt-10) REVERT: B 646 ASP cc_start: 0.7790 (t70) cc_final: 0.7320 (t0) REVERT: C 219 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8708 (tp) REVERT: C 389 THR cc_start: 0.8928 (t) cc_final: 0.8465 (p) REVERT: D 213 ASN cc_start: 0.8681 (t0) cc_final: 0.8431 (t0) REVERT: D 324 LYS cc_start: 0.8609 (pttm) cc_final: 0.8298 (ptpp) REVERT: D 327 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8140 (mt-10) REVERT: D 374 TYR cc_start: 0.8110 (t80) cc_final: 0.7773 (t80) REVERT: D 378 HIS cc_start: 0.8711 (OUTLIER) cc_final: 0.8210 (p90) REVERT: D 536 GLU cc_start: 0.8505 (mp0) cc_final: 0.8078 (mp0) REVERT: D 646 ASP cc_start: 0.7461 (t0) cc_final: 0.7208 (t0) REVERT: D 651 GLU cc_start: 0.7884 (tp30) cc_final: 0.7619 (tp30) REVERT: D 716 MET cc_start: 0.4819 (ptt) cc_final: 0.3969 (mmm) REVERT: D 730 PHE cc_start: 0.8176 (m-80) cc_final: 0.7892 (m-80) outliers start: 56 outliers final: 43 residues processed: 446 average time/residue: 0.3245 time to fit residues: 221.9227 Evaluate side-chains 439 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 394 time to evaluate : 2.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain B residue 720 PHE Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 390 CYS Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 733 ASP Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 568 MET Chi-restraints excluded: chain D residue 649 PHE Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 720 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 207 optimal weight: 0.6980 chunk 141 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 185 optimal weight: 6.9990 chunk 102 optimal weight: 0.6980 chunk 212 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 127 optimal weight: 3.9990 chunk 223 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 20 ASN C 213 ASN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 21851 Z= 0.385 Angle : 0.597 10.976 29528 Z= 0.314 Chirality : 0.042 0.180 3310 Planarity : 0.004 0.053 3665 Dihedral : 10.038 120.912 3104 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 3.03 % Allowed : 10.03 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.70 (0.17), residues: 2599 helix: 1.91 (0.14), residues: 1451 sheet: -0.06 (0.53), residues: 80 loop : -1.64 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 740 HIS 0.025 0.001 HIS D 378 PHE 0.018 0.002 PHE C 438 TYR 0.017 0.002 TYR A 453 ARG 0.007 0.001 ARG A 721 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 385 time to evaluate : 2.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8373 (t70) cc_final: 0.8053 (m-30) REVERT: A 220 LEU cc_start: 0.9343 (mm) cc_final: 0.9068 (mm) REVERT: A 710 LYS cc_start: 0.8828 (ttmt) cc_final: 0.8553 (tppt) REVERT: F 46 LYS cc_start: 0.8424 (mtmm) cc_final: 0.8105 (mtmm) REVERT: B 213 ASN cc_start: 0.8677 (t0) cc_final: 0.8206 (t0) REVERT: B 223 ASN cc_start: 0.8349 (m110) cc_final: 0.7930 (m110) REVERT: B 306 THR cc_start: 0.9402 (m) cc_final: 0.9171 (p) REVERT: B 361 GLU cc_start: 0.6984 (tp30) cc_final: 0.6741 (tp30) REVERT: B 392 LYS cc_start: 0.8567 (mmtt) cc_final: 0.8356 (mmtm) REVERT: B 646 ASP cc_start: 0.8001 (t70) cc_final: 0.7456 (t0) REVERT: D 213 ASN cc_start: 0.8693 (t0) cc_final: 0.8311 (t0) REVERT: D 428 ARG cc_start: 0.8071 (tpp80) cc_final: 0.7859 (tpp80) REVERT: D 536 GLU cc_start: 0.8471 (mp0) cc_final: 0.8001 (mp0) REVERT: D 568 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8725 (mtt) REVERT: D 646 ASP cc_start: 0.7654 (t0) cc_final: 0.7423 (t0) REVERT: D 716 MET cc_start: 0.4603 (ptt) cc_final: 0.3873 (mmm) REVERT: D 730 PHE cc_start: 0.8169 (m-80) cc_final: 0.7769 (m-80) outliers start: 70 outliers final: 57 residues processed: 426 average time/residue: 0.3315 time to fit residues: 216.7225 Evaluate side-chains 436 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 378 time to evaluate : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain F residue 25 MET Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain B residue 720 PHE Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 390 CYS Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 733 ASP Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 568 MET Chi-restraints excluded: chain D residue 649 PHE Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 720 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 83 optimal weight: 0.0070 chunk 224 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 146 optimal weight: 10.0000 chunk 61 optimal weight: 0.0020 chunk 249 optimal weight: 0.9980 chunk 207 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 131 optimal weight: 0.6980 overall best weight: 0.4806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 GLN F 20 ASN D 378 HIS ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21851 Z= 0.133 Angle : 0.509 11.677 29528 Z= 0.267 Chirality : 0.038 0.185 3310 Planarity : 0.003 0.046 3665 Dihedral : 9.596 122.031 3104 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.95 % Allowed : 11.41 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.96 (0.17), residues: 2599 helix: 2.15 (0.14), residues: 1455 sheet: 0.18 (0.55), residues: 80 loop : -1.58 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 740 HIS 0.003 0.001 HIS B 378 PHE 0.020 0.001 PHE C 582 TYR 0.013 0.001 TYR B 199 ARG 0.006 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 412 time to evaluate : 2.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8349 (t70) cc_final: 0.8040 (m-30) REVERT: A 181 ARG cc_start: 0.7571 (tpp80) cc_final: 0.7222 (mtm180) REVERT: A 220 LEU cc_start: 0.9339 (mm) cc_final: 0.9073 (mm) REVERT: A 361 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6737 (mt-10) REVERT: A 500 ARG cc_start: 0.8092 (tpt90) cc_final: 0.7828 (tpt-90) REVERT: A 584 TYR cc_start: 0.8978 (t80) cc_final: 0.8727 (t80) REVERT: A 710 LYS cc_start: 0.8774 (ttmt) cc_final: 0.8485 (tppt) REVERT: F 13 LYS cc_start: 0.8818 (mtmt) cc_final: 0.8371 (mtpt) REVERT: B 213 ASN cc_start: 0.8561 (t0) cc_final: 0.8140 (t0) REVERT: B 223 ASN cc_start: 0.8343 (m110) cc_final: 0.7910 (m110) REVERT: B 306 THR cc_start: 0.9349 (m) cc_final: 0.9126 (p) REVERT: B 392 LYS cc_start: 0.8485 (mmtt) cc_final: 0.8274 (mmtm) REVERT: B 646 ASP cc_start: 0.7747 (t70) cc_final: 0.7228 (t0) REVERT: C 213 ASN cc_start: 0.8180 (t0) cc_final: 0.7971 (t0) REVERT: C 219 LEU cc_start: 0.8954 (mm) cc_final: 0.8666 (tp) REVERT: C 472 TYR cc_start: 0.7008 (m-10) cc_final: 0.6731 (m-10) REVERT: D 213 ASN cc_start: 0.8582 (t0) cc_final: 0.8284 (t0) REVERT: D 428 ARG cc_start: 0.7985 (tpp80) cc_final: 0.7559 (tpp80) REVERT: D 536 GLU cc_start: 0.8469 (mp0) cc_final: 0.8054 (mp0) REVERT: D 646 ASP cc_start: 0.7432 (t0) cc_final: 0.7206 (t0) REVERT: D 651 GLU cc_start: 0.7763 (tp30) cc_final: 0.7560 (tp30) REVERT: D 716 MET cc_start: 0.4481 (ptt) cc_final: 0.3810 (mmm) REVERT: D 730 PHE cc_start: 0.8177 (m-80) cc_final: 0.7977 (m-10) outliers start: 45 outliers final: 39 residues processed: 436 average time/residue: 0.3397 time to fit residues: 226.8121 Evaluate side-chains 432 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 393 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain B residue 720 PHE Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 390 CYS Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 733 ASP Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 649 PHE Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 720 PHE Chi-restraints excluded: chain D residue 722 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 240 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 142 optimal weight: 8.9990 chunk 182 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 210 optimal weight: 7.9990 chunk 139 optimal weight: 0.8980 chunk 248 optimal weight: 0.2980 chunk 155 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 20 ASN B 676 ASN B 727 GLN D 358 HIS ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 21851 Z= 0.159 Angle : 0.510 10.945 29528 Z= 0.267 Chirality : 0.038 0.207 3310 Planarity : 0.003 0.047 3665 Dihedral : 9.280 121.241 3104 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 1.99 % Allowed : 11.76 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.17), residues: 2599 helix: 2.18 (0.14), residues: 1462 sheet: 0.28 (0.55), residues: 80 loop : -1.55 (0.19), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 740 HIS 0.002 0.000 HIS B 378 PHE 0.017 0.001 PHE C 582 TYR 0.012 0.001 TYR D 246 ARG 0.005 0.000 ARG C 211 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 414 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8374 (t70) cc_final: 0.8046 (m-30) REVERT: A 181 ARG cc_start: 0.7613 (tpp80) cc_final: 0.7316 (mtm180) REVERT: A 220 LEU cc_start: 0.9334 (mm) cc_final: 0.9076 (mm) REVERT: A 445 MET cc_start: 0.9229 (mmt) cc_final: 0.8895 (mmt) REVERT: A 500 ARG cc_start: 0.8074 (tpt90) cc_final: 0.7822 (tpt-90) REVERT: A 584 TYR cc_start: 0.8996 (t80) cc_final: 0.8696 (t80) REVERT: A 710 LYS cc_start: 0.8804 (ttmt) cc_final: 0.8567 (tppt) REVERT: F 13 LYS cc_start: 0.8817 (mtmt) cc_final: 0.8308 (mtpt) REVERT: B 213 ASN cc_start: 0.8504 (t0) cc_final: 0.8099 (t0) REVERT: B 223 ASN cc_start: 0.8359 (m110) cc_final: 0.7948 (m110) REVERT: B 306 THR cc_start: 0.9347 (m) cc_final: 0.9131 (p) REVERT: B 312 ILE cc_start: 0.9441 (OUTLIER) cc_final: 0.9230 (mp) REVERT: B 361 GLU cc_start: 0.7304 (tp30) cc_final: 0.6963 (tp30) REVERT: B 392 LYS cc_start: 0.8434 (mmtt) cc_final: 0.8217 (mmtm) REVERT: B 646 ASP cc_start: 0.7810 (t70) cc_final: 0.7196 (t0) REVERT: C 213 ASN cc_start: 0.8172 (t0) cc_final: 0.7208 (t0) REVERT: C 219 LEU cc_start: 0.8931 (mm) cc_final: 0.8633 (tp) REVERT: C 472 TYR cc_start: 0.7021 (m-10) cc_final: 0.6781 (m-10) REVERT: D 213 ASN cc_start: 0.8506 (t0) cc_final: 0.8011 (t0) REVERT: D 237 LYS cc_start: 0.8803 (mttp) cc_final: 0.8483 (mttp) REVERT: D 428 ARG cc_start: 0.7992 (tpp80) cc_final: 0.7575 (tpp80) REVERT: D 536 GLU cc_start: 0.8468 (mp0) cc_final: 0.8034 (mp0) REVERT: D 716 MET cc_start: 0.4410 (ptt) cc_final: 0.3751 (mmm) outliers start: 46 outliers final: 38 residues processed: 435 average time/residue: 0.3562 time to fit residues: 239.8861 Evaluate side-chains 435 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 396 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain B residue 720 PHE Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 390 CYS Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 720 PHE Chi-restraints excluded: chain C residue 733 ASP Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 649 PHE Chi-restraints excluded: chain D residue 720 PHE Chi-restraints excluded: chain D residue 722 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 153 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 148 optimal weight: 10.0000 chunk 74 optimal weight: 0.0060 chunk 48 optimal weight: 0.9980 chunk 158 optimal weight: 0.8980 chunk 169 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 195 optimal weight: 3.9990 chunk 226 optimal weight: 6.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 ASN ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 21851 Z= 0.146 Angle : 0.511 10.762 29528 Z= 0.267 Chirality : 0.038 0.207 3310 Planarity : 0.003 0.048 3665 Dihedral : 9.071 120.932 3104 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 1.60 % Allowed : 12.58 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.07 (0.17), residues: 2599 helix: 2.23 (0.14), residues: 1460 sheet: 0.36 (0.56), residues: 80 loop : -1.57 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 740 HIS 0.002 0.000 HIS D 358 PHE 0.018 0.001 PHE C 730 TYR 0.011 0.001 TYR B 199 ARG 0.005 0.000 ARG C 211 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 407 time to evaluate : 2.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8408 (t70) cc_final: 0.8052 (m-30) REVERT: A 181 ARG cc_start: 0.7611 (tpp80) cc_final: 0.7298 (mtm180) REVERT: A 220 LEU cc_start: 0.9357 (mm) cc_final: 0.9080 (mm) REVERT: A 445 MET cc_start: 0.9234 (mmt) cc_final: 0.8899 (mmt) REVERT: A 500 ARG cc_start: 0.8093 (tpt90) cc_final: 0.7830 (tpt-90) REVERT: A 584 TYR cc_start: 0.8965 (t80) cc_final: 0.8732 (t80) REVERT: A 710 LYS cc_start: 0.8791 (ttmt) cc_final: 0.8574 (tppt) REVERT: F 13 LYS cc_start: 0.8845 (mtmt) cc_final: 0.8276 (mttm) REVERT: B 213 ASN cc_start: 0.8491 (t0) cc_final: 0.8002 (t0) REVERT: B 216 LEU cc_start: 0.9347 (mt) cc_final: 0.9058 (mt) REVERT: B 223 ASN cc_start: 0.8342 (m110) cc_final: 0.7918 (m110) REVERT: B 361 GLU cc_start: 0.7307 (tp30) cc_final: 0.6946 (tp30) REVERT: B 646 ASP cc_start: 0.7645 (t70) cc_final: 0.7027 (t0) REVERT: C 213 ASN cc_start: 0.7838 (t0) cc_final: 0.7414 (t0) REVERT: C 219 LEU cc_start: 0.8885 (mm) cc_final: 0.8660 (tp) REVERT: C 472 TYR cc_start: 0.7014 (m-10) cc_final: 0.6809 (m-10) REVERT: D 213 ASN cc_start: 0.8218 (t0) cc_final: 0.7983 (t0) REVERT: D 428 ARG cc_start: 0.7966 (tpp80) cc_final: 0.7548 (tpp80) REVERT: D 536 GLU cc_start: 0.8468 (mp0) cc_final: 0.8002 (mp0) REVERT: D 716 MET cc_start: 0.4406 (ptt) cc_final: 0.3726 (mmm) outliers start: 37 outliers final: 33 residues processed: 427 average time/residue: 0.3343 time to fit residues: 219.8733 Evaluate side-chains 427 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 394 time to evaluate : 2.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain B residue 720 PHE Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 720 PHE Chi-restraints excluded: chain C residue 733 ASP Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 649 PHE Chi-restraints excluded: chain D residue 720 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 238 optimal weight: 1.9990 chunk 217 optimal weight: 7.9990 chunk 231 optimal weight: 0.3980 chunk 139 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 209 optimal weight: 0.9990 chunk 219 optimal weight: 0.6980 chunk 230 optimal weight: 0.7980 chunk 152 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 ASN B 727 GLN C 652 ASN ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21851 Z= 0.143 Angle : 0.512 10.827 29528 Z= 0.265 Chirality : 0.038 0.212 3310 Planarity : 0.003 0.052 3665 Dihedral : 8.806 119.997 3104 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 1.47 % Allowed : 12.62 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.09 (0.17), residues: 2599 helix: 2.23 (0.14), residues: 1461 sheet: 0.41 (0.56), residues: 80 loop : -1.52 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 740 HIS 0.003 0.000 HIS D 358 PHE 0.016 0.001 PHE C 582 TYR 0.010 0.001 TYR B 199 ARG 0.005 0.000 ARG C 211 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 409 time to evaluate : 2.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8402 (t70) cc_final: 0.8053 (m-30) REVERT: A 181 ARG cc_start: 0.7619 (tpp80) cc_final: 0.7163 (mtm180) REVERT: A 220 LEU cc_start: 0.9353 (mm) cc_final: 0.9067 (mm) REVERT: A 445 MET cc_start: 0.9254 (mmt) cc_final: 0.8924 (mmt) REVERT: A 584 TYR cc_start: 0.8948 (t80) cc_final: 0.8727 (t80) REVERT: A 710 LYS cc_start: 0.8769 (ttmt) cc_final: 0.8553 (tppt) REVERT: F 13 LYS cc_start: 0.8868 (mtmt) cc_final: 0.8377 (mttm) REVERT: B 213 ASN cc_start: 0.8452 (t0) cc_final: 0.7993 (t0) REVERT: B 216 LEU cc_start: 0.9337 (mt) cc_final: 0.9111 (mt) REVERT: B 223 ASN cc_start: 0.8367 (m110) cc_final: 0.7952 (m110) REVERT: B 242 ARG cc_start: 0.7722 (mpp-170) cc_final: 0.7431 (mpp-170) REVERT: B 312 ILE cc_start: 0.9417 (OUTLIER) cc_final: 0.9203 (mp) REVERT: B 361 GLU cc_start: 0.7299 (tp30) cc_final: 0.6957 (tp30) REVERT: C 213 ASN cc_start: 0.7581 (t0) cc_final: 0.7308 (t0) REVERT: C 219 LEU cc_start: 0.8863 (mm) cc_final: 0.8640 (tp) REVERT: D 213 ASN cc_start: 0.8173 (t0) cc_final: 0.7952 (t0) REVERT: D 428 ARG cc_start: 0.7930 (tpp80) cc_final: 0.7515 (tpp80) REVERT: D 536 GLU cc_start: 0.8472 (mp0) cc_final: 0.8011 (mp0) REVERT: D 716 MET cc_start: 0.4397 (ptt) cc_final: 0.3633 (mmm) outliers start: 34 outliers final: 30 residues processed: 428 average time/residue: 0.3319 time to fit residues: 216.6679 Evaluate side-chains 424 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 393 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain B residue 720 PHE Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 733 ASP Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 649 PHE Chi-restraints excluded: chain D residue 720 PHE Chi-restraints excluded: chain D residue 722 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 245 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 170 optimal weight: 0.8980 chunk 257 optimal weight: 0.8980 chunk 236 optimal weight: 4.9990 chunk 204 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 158 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 162 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 ASN ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21851 Z= 0.167 Angle : 0.533 11.538 29528 Z= 0.276 Chirality : 0.039 0.207 3310 Planarity : 0.004 0.047 3665 Dihedral : 8.710 119.018 3104 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 1.47 % Allowed : 13.32 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.14 (0.17), residues: 2599 helix: 2.27 (0.14), residues: 1452 sheet: 0.41 (0.56), residues: 80 loop : -1.48 (0.19), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 740 HIS 0.002 0.000 HIS B 378 PHE 0.018 0.001 PHE C 730 TYR 0.018 0.001 TYR C 246 ARG 0.005 0.000 ARG C 211 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 398 time to evaluate : 2.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8401 (t70) cc_final: 0.8056 (m-30) REVERT: A 181 ARG cc_start: 0.7615 (tpp80) cc_final: 0.7156 (mtm180) REVERT: A 220 LEU cc_start: 0.9355 (mm) cc_final: 0.9065 (mm) REVERT: A 226 ASP cc_start: 0.8290 (t0) cc_final: 0.7862 (t0) REVERT: A 445 MET cc_start: 0.9247 (mmt) cc_final: 0.8900 (mmt) REVERT: A 584 TYR cc_start: 0.8974 (t80) cc_final: 0.8699 (t80) REVERT: A 710 LYS cc_start: 0.8762 (ttmt) cc_final: 0.8552 (tppt) REVERT: F 13 LYS cc_start: 0.8867 (mtmt) cc_final: 0.8354 (mttm) REVERT: B 213 ASN cc_start: 0.8461 (t0) cc_final: 0.7997 (t0) REVERT: B 216 LEU cc_start: 0.9336 (mt) cc_final: 0.9106 (mt) REVERT: B 223 ASN cc_start: 0.8378 (m110) cc_final: 0.7976 (m110) REVERT: B 312 ILE cc_start: 0.9425 (OUTLIER) cc_final: 0.9207 (mp) REVERT: B 361 GLU cc_start: 0.7345 (tp30) cc_final: 0.7014 (tp30) REVERT: C 219 LEU cc_start: 0.8830 (mm) cc_final: 0.8602 (tp) REVERT: C 445 MET cc_start: 0.8510 (mmm) cc_final: 0.8266 (mmt) REVERT: D 237 LYS cc_start: 0.8733 (mttp) cc_final: 0.8463 (mmtm) REVERT: D 428 ARG cc_start: 0.7946 (tpp80) cc_final: 0.7517 (tpp80) REVERT: D 536 GLU cc_start: 0.8473 (mp0) cc_final: 0.8015 (mp0) REVERT: D 716 MET cc_start: 0.4410 (ptt) cc_final: 0.3637 (mmm) outliers start: 34 outliers final: 30 residues processed: 415 average time/residue: 0.3192 time to fit residues: 203.6236 Evaluate side-chains 422 residues out of total 2313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 391 time to evaluate : 2.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 649 PHE Chi-restraints excluded: chain D residue 720 PHE Chi-restraints excluded: chain D residue 722 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 218 optimal weight: 0.4980 chunk 62 optimal weight: 6.9990 chunk 188 optimal weight: 0.0170 chunk 30 optimal weight: 0.2980 chunk 56 optimal weight: 3.9990 chunk 205 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 210 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 overall best weight: 0.5620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 ASN ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.151594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.104552 restraints weight = 32861.596| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.70 r_work: 0.3059 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21851 Z= 0.136 Angle : 0.535 14.792 29528 Z= 0.273 Chirality : 0.038 0.200 3310 Planarity : 0.004 0.078 3665 Dihedral : 8.582 119.036 3104 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 1.56 % Allowed : 13.27 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.18 (0.17), residues: 2599 helix: 2.32 (0.14), residues: 1450 sheet: 0.41 (0.56), residues: 80 loop : -1.46 (0.19), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 740 HIS 0.002 0.000 HIS F 59 PHE 0.032 0.001 PHE D 730 TYR 0.016 0.001 TYR C 246 ARG 0.007 0.000 ARG D 212 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5296.40 seconds wall clock time: 95 minutes 37.62 seconds (5737.62 seconds total)