Starting phenix.real_space_refine on Fri Nov 17 09:30:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpa_23474/11_2023/7lpa_23474_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpa_23474/11_2023/7lpa_23474.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpa_23474/11_2023/7lpa_23474_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpa_23474/11_2023/7lpa_23474_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpa_23474/11_2023/7lpa_23474_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpa_23474/11_2023/7lpa_23474.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpa_23474/11_2023/7lpa_23474.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpa_23474/11_2023/7lpa_23474_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpa_23474/11_2023/7lpa_23474_neut_updated.pdb" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 16 5.49 5 S 100 5.16 5 Na 2 4.78 5 C 12272 2.51 5 N 2940 2.21 5 O 3304 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A GLU 326": "OE1" <-> "OE2" Residue "A ARG 331": "NH1" <-> "NH2" Residue "A GLU 359": "OE1" <-> "OE2" Residue "A GLU 361": "OE1" <-> "OE2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "A TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A ARG 420": "NH1" <-> "NH2" Residue "A PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 471": "OD1" <-> "OD2" Residue "A ARG 474": "NH1" <-> "NH2" Residue "A TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 491": "NH1" <-> "NH2" Residue "A PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 513": "OE1" <-> "OE2" Residue "A TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 557": "NH1" <-> "NH2" Residue "A GLU 570": "OE1" <-> "OE2" Residue "A PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 636": "OE1" <-> "OE2" Residue "A ASP 646": "OD1" <-> "OD2" Residue "A PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B GLU 326": "OE1" <-> "OE2" Residue "B ARG 331": "NH1" <-> "NH2" Residue "B GLU 359": "OE1" <-> "OE2" Residue "B GLU 361": "OE1" <-> "OE2" Residue "B GLU 371": "OE1" <-> "OE2" Residue "B TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 409": "NH1" <-> "NH2" Residue "B ARG 420": "NH1" <-> "NH2" Residue "B PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 471": "OD1" <-> "OD2" Residue "B ARG 474": "NH1" <-> "NH2" Residue "B TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 491": "NH1" <-> "NH2" Residue "B PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 513": "OE1" <-> "OE2" Residue "B TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B GLU 570": "OE1" <-> "OE2" Residue "B PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 636": "OE1" <-> "OE2" Residue "B ASP 646": "OD1" <-> "OD2" Residue "B PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 311": "OE1" <-> "OE2" Residue "C GLU 326": "OE1" <-> "OE2" Residue "C ARG 331": "NH1" <-> "NH2" Residue "C GLU 359": "OE1" <-> "OE2" Residue "C GLU 361": "OE1" <-> "OE2" Residue "C GLU 371": "OE1" <-> "OE2" Residue "C TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 409": "NH1" <-> "NH2" Residue "C ARG 420": "NH1" <-> "NH2" Residue "C PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 471": "OD1" <-> "OD2" Residue "C ARG 474": "NH1" <-> "NH2" Residue "C TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 491": "NH1" <-> "NH2" Residue "C PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 513": "OE1" <-> "OE2" Residue "C TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 557": "NH1" <-> "NH2" Residue "C GLU 570": "OE1" <-> "OE2" Residue "C PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 636": "OE1" <-> "OE2" Residue "C ASP 646": "OD1" <-> "OD2" Residue "C PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 311": "OE1" <-> "OE2" Residue "D GLU 326": "OE1" <-> "OE2" Residue "D ARG 331": "NH1" <-> "NH2" Residue "D GLU 359": "OE1" <-> "OE2" Residue "D GLU 361": "OE1" <-> "OE2" Residue "D GLU 371": "OE1" <-> "OE2" Residue "D TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 409": "NH1" <-> "NH2" Residue "D ARG 420": "NH1" <-> "NH2" Residue "D PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 471": "OD1" <-> "OD2" Residue "D ARG 474": "NH1" <-> "NH2" Residue "D TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 491": "NH1" <-> "NH2" Residue "D PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 513": "OE1" <-> "OE2" Residue "D TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 557": "NH1" <-> "NH2" Residue "D GLU 570": "OE1" <-> "OE2" Residue "D PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 636": "OE1" <-> "OE2" Residue "D ASP 646": "OD1" <-> "OD2" Residue "D PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 18634 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4467 Classifications: {'peptide': 598} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 109} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 582} Chain breaks: 5 Unresolved non-hydrogen bonds: 379 Unresolved non-hydrogen angles: 477 Unresolved non-hydrogen dihedrals: 296 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 217 Chain: "B" Number of atoms: 4467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4467 Classifications: {'peptide': 598} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 109} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 582} Chain breaks: 5 Unresolved non-hydrogen bonds: 379 Unresolved non-hydrogen angles: 477 Unresolved non-hydrogen dihedrals: 296 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 217 Chain: "C" Number of atoms: 4467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4467 Classifications: {'peptide': 598} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 109} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 582} Chain breaks: 5 Unresolved non-hydrogen bonds: 379 Unresolved non-hydrogen angles: 477 Unresolved non-hydrogen dihedrals: 296 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 217 Chain: "D" Number of atoms: 4467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4467 Classifications: {'peptide': 598} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 109} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 582} Chain breaks: 5 Unresolved non-hydrogen bonds: 379 Unresolved non-hydrogen angles: 477 Unresolved non-hydrogen dihedrals: 296 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 217 Chain: "A" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 224 Unusual residues: {' NA': 2, '4DY': 1, '6OU': 4, 'LBN': 2, 'YFP': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'YFP:plan-3': 1, 'LBN:plan-3': 2, '6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 191 Unusual residues: {'4DY': 1, '6OU': 3, 'LBN': 2, 'YFP': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'YFP:plan-3': 1, 'LBN:plan-3': 2, '6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 191 Unusual residues: {'4DY': 1, '6OU': 3, 'LBN': 2, 'YFP': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'YFP:plan-3': 1, 'LBN:plan-3': 2, '6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 160 Unusual residues: {'4DY': 1, '6OU': 2, 'LBN': 2, 'YFP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'YFP:plan-3': 1, 'LBN:plan-3': 2, '6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 14 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ALA A 204 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA A 204 " occ=0.50 residue: pdb=" N ALA B 204 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA B 204 " occ=0.50 residue: pdb=" N ALA C 204 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA C 204 " occ=0.50 residue: pdb=" N ALA D 204 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA D 204 " occ=0.50 Time building chain proxies: 11.03, per 1000 atoms: 0.59 Number of scatterers: 18634 At special positions: 0 Unit cell: (122.04, 122.04, 117.72, 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 100 16.00 P 16 15.00 Na 2 11.00 O 3304 8.00 N 2940 7.00 C 12272 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 390 " distance=2.04 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 390 " distance=2.04 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 390 " distance=2.04 Simple disulfide: pdb=" SG CYS D 386 " - pdb=" SG CYS D 390 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.92 Conformation dependent library (CDL) restraints added in 3.7 seconds 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4536 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 8 sheets defined 58.4% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'A' and resid 114 through 123 Processing helix chain 'A' and resid 127 through 138 Proline residue: A 134 - end of helix Processing helix chain 'A' and resid 157 through 163 Processing helix chain 'A' and resid 172 through 182 Processing helix chain 'A' and resid 204 through 211 removed outlier: 3.588A pdb=" N ARG A 211 " --> pdb=" O ILE A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 223 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 294 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 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 411 through 413 No H-bonds generated for 'chain 'A' and resid 411 through 413' Processing helix chain 'A' and resid 416 through 428 Processing helix chain 'A' and resid 431 through 452 Processing helix chain 'A' and resid 469 through 499 Processing helix chain 'A' and resid 506 through 509 No H-bonds generated for 'chain 'A' and resid 506 through 509' Processing helix chain 'A' and resid 512 through 530 Processing helix chain 'A' and resid 535 through 557 removed outlier: 3.846A pdb=" N VAL A 538 " --> pdb=" O LYS A 535 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL A 542 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 553 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG A 557 " --> pdb=" O TYR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 596 removed outlier: 4.194A pdb=" N TYR A 565 " --> pdb=" O GLN A 561 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 642 removed outlier: 4.216A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE A 642 " --> pdb=" O PHE A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 670 Processing helix chain 'A' and resid 674 through 689 Processing helix chain 'A' and resid 692 through 713 Processing helix chain 'B' and resid 114 through 123 Processing helix chain 'B' and resid 127 through 138 Proline residue: B 134 - end of helix Processing helix chain 'B' and resid 157 through 163 Processing helix chain 'B' and resid 172 through 182 Processing helix chain 'B' and resid 204 through 211 removed outlier: 3.589A pdb=" N ARG B 211 " --> pdb=" O ILE B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 223 Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' 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 294 Processing helix chain 'B' and resid 299 through 319 Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 346 through 354 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 413 No H-bonds generated for 'chain 'B' and resid 411 through 413' Processing helix chain 'B' and resid 416 through 428 Processing helix chain 'B' and resid 431 through 452 Processing helix chain 'B' and resid 469 through 499 Processing helix chain 'B' and resid 506 through 509 No H-bonds generated for 'chain 'B' and resid 506 through 509' Processing helix chain 'B' and resid 512 through 530 Processing helix chain 'B' and resid 535 through 557 removed outlier: 3.846A pdb=" N VAL B 538 " --> pdb=" O LYS B 535 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 553 " --> pdb=" O THR B 550 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG B 557 " --> pdb=" O TYR B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 596 removed outlier: 4.194A pdb=" N TYR B 565 " --> pdb=" O GLN B 561 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 642 removed outlier: 4.216A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE B 642 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 670 Processing helix chain 'B' and resid 674 through 689 Processing helix chain 'B' and resid 692 through 713 Processing helix chain 'C' and resid 114 through 123 Processing helix chain 'C' and resid 127 through 138 Proline residue: C 134 - end of helix Processing helix chain 'C' and resid 157 through 163 Processing helix chain 'C' and resid 172 through 182 Processing helix chain 'C' and resid 204 through 211 removed outlier: 3.588A pdb=" N ARG C 211 " --> pdb=" O ILE C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 223 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 294 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 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 411 through 413 No H-bonds generated for 'chain 'C' and resid 411 through 413' Processing helix chain 'C' and resid 416 through 428 Processing helix chain 'C' and resid 431 through 452 Processing helix chain 'C' and resid 469 through 499 Processing helix chain 'C' and resid 506 through 509 No H-bonds generated for 'chain 'C' and resid 506 through 509' Processing helix chain 'C' and resid 512 through 530 Processing helix chain 'C' and resid 535 through 557 removed outlier: 3.846A pdb=" N VAL C 538 " --> pdb=" O LYS C 535 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 553 " --> pdb=" O THR C 550 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG C 557 " --> pdb=" O TYR C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 596 removed outlier: 4.194A pdb=" N TYR C 565 " --> pdb=" O GLN C 561 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 642 removed outlier: 4.215A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE C 642 " --> pdb=" O PHE C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 670 Processing helix chain 'C' and resid 674 through 689 Processing helix chain 'C' and resid 692 through 713 Processing helix chain 'D' and resid 114 through 123 Processing helix chain 'D' and resid 127 through 138 Proline residue: D 134 - end of helix Processing helix chain 'D' and resid 157 through 163 Processing helix chain 'D' and resid 172 through 182 Processing helix chain 'D' and resid 204 through 211 removed outlier: 3.588A pdb=" N ARG D 211 " --> pdb=" O ILE D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 223 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 294 Processing helix chain 'D' and resid 299 through 319 Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 346 through 354 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 411 through 413 No H-bonds generated for 'chain 'D' and resid 411 through 413' Processing helix chain 'D' and resid 416 through 428 Processing helix chain 'D' and resid 431 through 452 Processing helix chain 'D' and resid 469 through 499 Processing helix chain 'D' and resid 506 through 509 No H-bonds generated for 'chain 'D' and resid 506 through 509' Processing helix chain 'D' and resid 512 through 530 Processing helix chain 'D' and resid 535 through 557 removed outlier: 3.846A pdb=" N VAL D 538 " --> pdb=" O LYS D 535 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL D 542 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU D 553 " --> pdb=" O THR D 550 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG D 557 " --> pdb=" O TYR D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 596 removed outlier: 4.195A pdb=" N TYR D 565 " --> pdb=" O GLN D 561 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 642 removed outlier: 4.216A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE D 642 " --> pdb=" O PHE D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 670 Processing helix chain 'D' and resid 674 through 689 Processing helix chain 'D' and resid 692 through 713 Processing sheet with id= A, first strand: chain 'A' and resid 742 through 747 removed outlier: 3.526A pdb=" N TRP A 372 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 724 through 727 Processing sheet with id= C, first strand: chain 'B' and resid 742 through 747 removed outlier: 3.526A pdb=" N TRP B 372 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 724 through 727 Processing sheet with id= E, first strand: chain 'C' and resid 742 through 747 removed outlier: 3.526A pdb=" N TRP C 372 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 724 through 727 Processing sheet with id= G, first strand: chain 'D' and resid 742 through 747 removed outlier: 3.526A pdb=" N TRP D 372 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 724 through 727 968 hydrogen bonds defined for protein. 2688 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: 5.51 Time building geometry restraints manager: 8.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2832 1.31 - 1.43: 5307 1.43 - 1.56: 10523 1.56 - 1.69: 154 1.69 - 1.81: 192 Bond restraints: 19008 Sorted by residual: bond pdb=" O2 LBN B 903 " pdb=" P1 LBN B 903 " ideal model delta sigma weight residual 1.650 1.788 -0.138 2.00e-02 2.50e+03 4.73e+01 bond pdb=" O2 LBN A 901 " pdb=" P1 LBN A 901 " ideal model delta sigma weight residual 1.650 1.787 -0.137 2.00e-02 2.50e+03 4.69e+01 bond pdb=" O2 LBN D 903 " pdb=" P1 LBN D 903 " ideal model delta sigma weight residual 1.650 1.787 -0.137 2.00e-02 2.50e+03 4.67e+01 bond pdb=" O2 LBN C 903 " pdb=" P1 LBN C 903 " ideal model delta sigma weight residual 1.650 1.787 -0.137 2.00e-02 2.50e+03 4.67e+01 bond pdb=" O22 6OU B 904 " pdb=" P23 6OU B 904 " ideal model delta sigma weight residual 1.643 1.773 -0.130 2.00e-02 2.50e+03 4.24e+01 ... (remaining 19003 not shown) Histogram of bond angle deviations from ideal: 98.91 - 105.94: 301 105.94 - 112.96: 9871 112.96 - 119.98: 6884 119.98 - 127.01: 8490 127.01 - 134.03: 162 Bond angle restraints: 25708 Sorted by residual: angle pdb=" O1 LBN C 903 " pdb=" P1 LBN C 903 " pdb=" O2 LBN C 903 " ideal model delta sigma weight residual 93.45 107.89 -14.44 3.00e+00 1.11e-01 2.32e+01 angle pdb=" O1 LBN D 903 " pdb=" P1 LBN D 903 " pdb=" O2 LBN D 903 " ideal model delta sigma weight residual 93.45 107.88 -14.43 3.00e+00 1.11e-01 2.31e+01 angle pdb=" O1 LBN A 901 " pdb=" P1 LBN A 901 " pdb=" O2 LBN A 901 " ideal model delta sigma weight residual 93.45 107.87 -14.42 3.00e+00 1.11e-01 2.31e+01 angle pdb=" O1 LBN B 903 " pdb=" P1 LBN B 903 " pdb=" O2 LBN B 903 " ideal model delta sigma weight residual 93.45 107.85 -14.40 3.00e+00 1.11e-01 2.30e+01 angle pdb=" O22 6OU B 904 " pdb=" P23 6OU B 904 " pdb=" O26 6OU B 904 " ideal model delta sigma weight residual 93.95 105.85 -11.90 3.00e+00 1.11e-01 1.57e+01 ... (remaining 25703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.81: 10653 33.81 - 67.63: 356 67.63 - 101.44: 38 101.44 - 135.25: 4 135.25 - 169.07: 13 Dihedral angle restraints: 11064 sinusoidal: 4036 harmonic: 7028 Sorted by residual: dihedral pdb=" C09 6OU B 904 " pdb=" C10 6OU B 904 " pdb=" C11 6OU B 904 " pdb=" C12 6OU B 904 " ideal model delta sinusoidal sigma weight residual 179.71 -11.22 -169.07 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" CA PHE C 247 " pdb=" C PHE C 247 " pdb=" N GLY C 248 " pdb=" CA GLY C 248 " ideal model delta harmonic sigma weight residual -180.00 -157.10 -22.90 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA PHE B 247 " pdb=" C PHE B 247 " pdb=" N GLY B 248 " pdb=" CA GLY B 248 " ideal model delta harmonic sigma weight residual -180.00 -157.15 -22.85 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 11061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2861 0.094 - 0.189: 35 0.189 - 0.283: 4 0.283 - 0.377: 6 0.377 - 0.471: 10 Chirality restraints: 2916 Sorted by residual: chirality pdb=" C2 LBN B 901 " pdb=" C1 LBN B 901 " pdb=" C3 LBN B 901 " pdb=" O7 LBN B 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.84 0.47 2.00e-01 2.50e+01 5.56e+00 chirality pdb=" C2 LBN A 907 " pdb=" C1 LBN A 907 " pdb=" C3 LBN A 907 " pdb=" O7 LBN A 907 " both_signs ideal model delta sigma weight residual False -2.36 -2.84 0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" C2 LBN C 901 " pdb=" C1 LBN C 901 " pdb=" C3 LBN C 901 " pdb=" O7 LBN C 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.84 0.47 2.00e-01 2.50e+01 5.54e+00 ... (remaining 2913 not shown) Planarity restraints: 3172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET D 541 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.53e+00 pdb=" C MET D 541 " 0.037 2.00e-02 2.50e+03 pdb=" O MET D 541 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL D 542 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 541 " 0.011 2.00e-02 2.50e+03 2.12e-02 4.47e+00 pdb=" C MET B 541 " -0.037 2.00e-02 2.50e+03 pdb=" O MET B 541 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL B 542 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 541 " 0.011 2.00e-02 2.50e+03 2.10e-02 4.40e+00 pdb=" C MET A 541 " -0.036 2.00e-02 2.50e+03 pdb=" O MET A 541 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL A 542 " 0.012 2.00e-02 2.50e+03 ... (remaining 3169 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1934 2.74 - 3.28: 19002 3.28 - 3.82: 29160 3.82 - 4.36: 34076 4.36 - 4.90: 59562 Nonbonded interactions: 143734 Sorted by model distance: nonbonded pdb=" OH TYR B 555 " pdb=" O4 LBN B 903 " model vdw 2.201 2.440 nonbonded pdb=" OH TYR C 555 " pdb=" O4 LBN C 903 " model vdw 2.201 2.440 nonbonded pdb=" OH TYR A 555 " pdb=" O4 LBN A 901 " model vdw 2.202 2.440 nonbonded pdb=" OH TYR D 555 " pdb=" O4 LBN D 903 " model vdw 2.202 2.440 nonbonded pdb=" N GLU D 356 " pdb=" OE1 GLU D 356 " model vdw 2.237 2.520 ... (remaining 143729 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 113 through 752 or (resid 901 and (name C1 or name C2 or n \ ame C25 or name C26 or name C27 or name C28 or name C29 or name C3 or name C30 o \ r name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C \ 37 or name C38 or name C39 or name O5 or name O6 or name O7 or name O8 )) or res \ id 904)) selection = (chain 'B' and (resid 113 through 752 or (resid 901 and (name C1 or name C2 or n \ ame C25 or name C26 or name C27 or name C28 or name C29 or name C3 or name C30 o \ r name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C \ 37 or name C38 or name C39 or name O5 or name O6 or name O7 or name O8 )) or (re \ sid 904 and (name C31 or name C33 or name C34 or name C35 or name C36 or name C3 \ 7 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or nam \ e O32)))) selection = (chain 'C' and (resid 113 through 752 or (resid 901 and (name C1 or name C2 or n \ ame C25 or name C26 or name C27 or name C28 or name C29 or name C3 or name C30 o \ r name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C \ 37 or name C38 or name C39 or name O5 or name O6 or name O7 or name O8 )) or (re \ sid 904 and (name C31 or name C33 or name C34 or name C35 or name C36 or name C3 \ 7 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or nam \ e O32)))) selection = (chain 'D' and (resid 113 through 752 or (resid 901 and (name C1 or name C2 or n \ ame C25 or name C26 or name C27 or name C28 or name C29 or name C3 or name C30 o \ r name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C \ 37 or name C38 or name C39 or name O5 or name O6 or name O7 or name O8 )) or (re \ sid 904 and (name C31 or name C33 or name C34 or name C35 or name C36 or name C3 \ 7 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or nam \ e O32)))) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.770 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 51.750 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 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 : 0.009 0.138 19008 Z= 0.553 Angle : 0.885 14.438 25708 Z= 0.390 Chirality : 0.047 0.471 2916 Planarity : 0.004 0.033 3172 Dihedral : 17.792 169.067 6516 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.82 (0.17), residues: 2344 helix: 0.54 (0.13), residues: 1424 sheet: -2.34 (0.44), residues: 116 loop : -2.23 (0.20), residues: 804 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 2.013 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.2825 time to fit residues: 135.0411 Evaluate side-chains 221 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 2.185 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 184 optimal weight: 30.0000 chunk 71 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 214 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN B 494 GLN C 494 GLN D 494 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19008 Z= 0.210 Angle : 0.510 4.741 25708 Z= 0.277 Chirality : 0.038 0.146 2916 Planarity : 0.004 0.039 3172 Dihedral : 16.673 164.898 3004 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.85 % Allowed : 6.58 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.10 (0.17), residues: 2344 helix: 0.96 (0.13), residues: 1432 sheet: -1.96 (0.43), residues: 116 loop : -1.64 (0.21), residues: 796 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 257 time to evaluate : 2.088 Fit side-chains outliers start: 31 outliers final: 27 residues processed: 272 average time/residue: 0.2887 time to fit residues: 125.0177 Evaluate side-chains 252 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 225 time to evaluate : 2.187 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1786 time to fit residues: 12.3487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 178 optimal weight: 20.0000 chunk 145 optimal weight: 0.6980 chunk 59 optimal weight: 40.0000 chunk 214 optimal weight: 4.9990 chunk 231 optimal weight: 0.9990 chunk 191 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 172 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19008 Z= 0.246 Angle : 0.508 4.824 25708 Z= 0.274 Chirality : 0.039 0.150 2916 Planarity : 0.004 0.039 3172 Dihedral : 15.696 166.160 3004 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.36 % Allowed : 10.77 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.10 (0.17), residues: 2344 helix: 1.01 (0.13), residues: 1432 sheet: -1.72 (0.45), residues: 116 loop : -1.35 (0.22), residues: 796 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 252 time to evaluate : 2.861 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 257 average time/residue: 0.3069 time to fit residues: 125.7791 Evaluate side-chains 231 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 225 time to evaluate : 2.370 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1758 time to fit residues: 5.1213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 228 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 204 optimal weight: 5.9990 chunk 61 optimal weight: 0.0770 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 494 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19008 Z= 0.137 Angle : 0.432 4.855 25708 Z= 0.237 Chirality : 0.036 0.155 2916 Planarity : 0.003 0.039 3172 Dihedral : 14.110 165.131 3004 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.66 % Allowed : 12.98 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.72 (0.18), residues: 2344 helix: 1.48 (0.14), residues: 1428 sheet: -1.51 (0.45), residues: 116 loop : -1.01 (0.23), residues: 800 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 259 time to evaluate : 2.060 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 260 average time/residue: 0.2725 time to fit residues: 113.2166 Evaluate side-chains 240 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 230 time to evaluate : 2.013 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1679 time to fit residues: 6.0002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 169 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 194 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 116 optimal weight: 8.9990 chunk 204 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19008 Z= 0.172 Angle : 0.444 5.561 25708 Z= 0.241 Chirality : 0.037 0.173 2916 Planarity : 0.003 0.039 3172 Dihedral : 13.344 164.276 3004 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.26 % Allowed : 14.71 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.75 (0.18), residues: 2344 helix: 1.45 (0.14), residues: 1440 sheet: -1.38 (0.46), residues: 116 loop : -0.94 (0.23), residues: 788 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 245 time to evaluate : 2.163 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 17 residues processed: 255 average time/residue: 0.2813 time to fit residues: 113.7073 Evaluate side-chains 248 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 231 time to evaluate : 2.034 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1692 time to fit residues: 8.4078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 10.0000 chunk 205 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 228 optimal weight: 2.9990 chunk 189 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 119 optimal weight: 20.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19008 Z= 0.282 Angle : 0.511 4.860 25708 Z= 0.272 Chirality : 0.039 0.188 2916 Planarity : 0.004 0.039 3172 Dihedral : 13.281 165.767 3004 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.90 % Allowed : 16.15 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.51 (0.17), residues: 2344 helix: 1.23 (0.13), residues: 1428 sheet: -1.29 (0.45), residues: 116 loop : -0.98 (0.23), residues: 800 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 240 time to evaluate : 2.115 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 15 residues processed: 245 average time/residue: 0.2811 time to fit residues: 109.4139 Evaluate side-chains 243 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 228 time to evaluate : 2.083 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1779 time to fit residues: 7.8594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 166 optimal weight: 0.6980 chunk 129 optimal weight: 3.9990 chunk 192 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 227 optimal weight: 0.8980 chunk 142 optimal weight: 10.0000 chunk 138 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19008 Z= 0.173 Angle : 0.450 4.874 25708 Z= 0.244 Chirality : 0.037 0.190 2916 Planarity : 0.003 0.040 3172 Dihedral : 12.746 165.709 3004 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.54 % Allowed : 16.93 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.76 (0.18), residues: 2344 helix: 1.43 (0.13), residues: 1440 sheet: -1.24 (0.45), residues: 116 loop : -0.93 (0.23), residues: 788 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 236 time to evaluate : 1.910 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 238 average time/residue: 0.2663 time to fit residues: 101.3384 Evaluate side-chains 231 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 223 time to evaluate : 2.044 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1653 time to fit residues: 5.3411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 144 optimal weight: 0.7980 chunk 154 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 178 optimal weight: 20.0000 chunk 206 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19008 Z= 0.207 Angle : 0.469 4.874 25708 Z= 0.252 Chirality : 0.037 0.205 2916 Planarity : 0.003 0.040 3172 Dihedral : 12.629 166.036 3004 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.24 % Allowed : 17.94 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.74 (0.17), residues: 2344 helix: 1.41 (0.13), residues: 1440 sheet: -1.13 (0.45), residues: 116 loop : -0.94 (0.23), residues: 788 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 237 time to evaluate : 2.297 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 238 average time/residue: 0.2746 time to fit residues: 105.5648 Evaluate side-chains 224 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 220 time to evaluate : 2.043 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1667 time to fit residues: 4.0866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 chunk 211 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 166 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 191 optimal weight: 6.9990 chunk 200 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 224 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19008 Z= 0.275 Angle : 0.522 6.100 25708 Z= 0.277 Chirality : 0.039 0.211 2916 Planarity : 0.004 0.040 3172 Dihedral : 12.947 166.655 3004 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.78 % Allowed : 18.78 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2344 helix: 1.25 (0.13), residues: 1440 sheet: -1.14 (0.45), residues: 116 loop : -1.13 (0.23), residues: 788 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 230 time to evaluate : 1.980 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 232 average time/residue: 0.2663 time to fit residues: 99.6109 Evaluate side-chains 240 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 229 time to evaluate : 2.032 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1685 time to fit residues: 6.3539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 0.8980 chunk 106 optimal weight: 0.0060 chunk 155 optimal weight: 2.9990 chunk 235 optimal weight: 10.0000 chunk 216 optimal weight: 0.8980 chunk 187 optimal weight: 20.0000 chunk 19 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 148 optimal weight: 0.9980 chunk 199 optimal weight: 8.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19008 Z= 0.146 Angle : 0.444 5.159 25708 Z= 0.242 Chirality : 0.037 0.205 2916 Planarity : 0.003 0.040 3172 Dihedral : 12.268 165.883 3004 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.18 % Allowed : 18.90 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.95 (0.18), residues: 2344 helix: 1.61 (0.14), residues: 1440 sheet: -0.99 (0.46), residues: 116 loop : -0.94 (0.23), residues: 788 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 241 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 242 average time/residue: 0.2748 time to fit residues: 107.0035 Evaluate side-chains 236 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 233 time to evaluate : 2.204 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1861 time to fit residues: 4.1414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 187 optimal weight: 20.0000 chunk 78 optimal weight: 4.9990 chunk 192 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.245134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.210046 restraints weight = 20780.225| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 1.20 r_work: 0.4093 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work: 0.4035 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4028 r_free = 0.4028 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4028 r_free = 0.4028 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 19008 Z= 0.312 Angle : 0.545 10.049 25708 Z= 0.288 Chirality : 0.040 0.214 2916 Planarity : 0.004 0.040 3172 Dihedral : 12.827 166.700 3004 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.84 % Allowed : 19.80 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.50 (0.17), residues: 2344 helix: 1.27 (0.13), residues: 1440 sheet: -1.06 (0.45), residues: 116 loop : -1.17 (0.23), residues: 788 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3599.36 seconds wall clock time: 66 minutes 17.92 seconds (3977.92 seconds total)