Starting phenix.real_space_refine on Sat Feb 17 05:12:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n17_24115/02_2024/7n17_24115_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n17_24115/02_2024/7n17_24115.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n17_24115/02_2024/7n17_24115.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n17_24115/02_2024/7n17_24115.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n17_24115/02_2024/7n17_24115_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n17_24115/02_2024/7n17_24115_updated.pdb" } resolution = 3.1 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= 0.006 sd= 0.100 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 96 5.16 5 C 11520 2.51 5 N 2872 2.21 5 O 3096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ARG 106": "NH1" <-> "NH2" Residue "A TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 191": "OD1" <-> "OD2" Residue "A ASP 229": "OD1" <-> "OD2" Residue "A GLU 236": "OE1" <-> "OE2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A ARG 286": "NH1" <-> "NH2" Residue "A TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A ASP 473": "OD1" <-> "OD2" Residue "A GLU 478": "OE1" <-> "OE2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A GLU 498": "OE1" <-> "OE2" Residue "A PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 518": "OD1" <-> "OD2" Residue "A ASP 525": "OD1" <-> "OD2" Residue "A GLU 529": "OE1" <-> "OE2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "A ASP 542": "OD1" <-> "OD2" Residue "A ASP 543": "OD1" <-> "OD2" Residue "A ASP 544": "OD1" <-> "OD2" Residue "A GLU 560": "OE1" <-> "OE2" Residue "A ARG 580": "NH1" <-> "NH2" Residue "A GLU 601": "OE1" <-> "OE2" Residue "A ASP 604": "OD1" <-> "OD2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A GLU 615": "OE1" <-> "OE2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B ARG 106": "NH1" <-> "NH2" Residue "B TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 191": "OD1" <-> "OD2" Residue "B ASP 229": "OD1" <-> "OD2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B GLU 238": "OE1" <-> "OE2" Residue "B ARG 286": "NH1" <-> "NH2" Residue "B TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 423": "OE1" <-> "OE2" Residue "B ASP 473": "OD1" <-> "OD2" Residue "B GLU 478": "OE1" <-> "OE2" Residue "B GLU 486": "OE1" <-> "OE2" Residue "B ARG 492": "NH1" <-> "NH2" Residue "B GLU 498": "OE1" <-> "OE2" Residue "B PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 518": "OD1" <-> "OD2" Residue "B ASP 525": "OD1" <-> "OD2" Residue "B GLU 529": "OE1" <-> "OE2" Residue "B ARG 535": "NH1" <-> "NH2" Residue "B ARG 537": "NH1" <-> "NH2" Residue "B ASP 542": "OD1" <-> "OD2" Residue "B ASP 543": "OD1" <-> "OD2" Residue "B ASP 544": "OD1" <-> "OD2" Residue "B GLU 560": "OE1" <-> "OE2" Residue "B ARG 580": "NH1" <-> "NH2" Residue "B GLU 601": "OE1" <-> "OE2" Residue "B ASP 604": "OD1" <-> "OD2" Residue "B ARG 606": "NH1" <-> "NH2" Residue "B GLU 615": "OE1" <-> "OE2" Residue "C ARG 104": "NH1" <-> "NH2" Residue "C ARG 106": "NH1" <-> "NH2" Residue "C TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 191": "OD1" <-> "OD2" Residue "C ASP 229": "OD1" <-> "OD2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "C GLU 238": "OE1" <-> "OE2" Residue "C ARG 286": "NH1" <-> "NH2" Residue "C TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 423": "OE1" <-> "OE2" Residue "C ASP 473": "OD1" <-> "OD2" Residue "C GLU 478": "OE1" <-> "OE2" Residue "C GLU 486": "OE1" <-> "OE2" Residue "C ARG 492": "NH1" <-> "NH2" Residue "C GLU 498": "OE1" <-> "OE2" Residue "C PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 518": "OD1" <-> "OD2" Residue "C ASP 525": "OD1" <-> "OD2" Residue "C GLU 529": "OE1" <-> "OE2" Residue "C ARG 535": "NH1" <-> "NH2" Residue "C ARG 537": "NH1" <-> "NH2" Residue "C ASP 542": "OD1" <-> "OD2" Residue "C ASP 543": "OD1" <-> "OD2" Residue "C ASP 544": "OD1" <-> "OD2" Residue "C GLU 560": "OE1" <-> "OE2" Residue "C ARG 580": "NH1" <-> "NH2" Residue "C GLU 601": "OE1" <-> "OE2" Residue "C ASP 604": "OD1" <-> "OD2" Residue "C ARG 606": "NH1" <-> "NH2" Residue "C GLU 615": "OE1" <-> "OE2" Residue "D ARG 104": "NH1" <-> "NH2" Residue "D ARG 106": "NH1" <-> "NH2" Residue "D TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 191": "OD1" <-> "OD2" Residue "D ASP 229": "OD1" <-> "OD2" Residue "D GLU 236": "OE1" <-> "OE2" Residue "D GLU 238": "OE1" <-> "OE2" Residue "D ARG 286": "NH1" <-> "NH2" Residue "D TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 423": "OE1" <-> "OE2" Residue "D ASP 473": "OD1" <-> "OD2" Residue "D GLU 478": "OE1" <-> "OE2" Residue "D GLU 486": "OE1" <-> "OE2" Residue "D ARG 492": "NH1" <-> "NH2" Residue "D GLU 498": "OE1" <-> "OE2" Residue "D PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 518": "OD1" <-> "OD2" Residue "D ASP 525": "OD1" <-> "OD2" Residue "D GLU 529": "OE1" <-> "OE2" Residue "D ARG 535": "NH1" <-> "NH2" Residue "D ARG 537": "NH1" <-> "NH2" Residue "D ASP 542": "OD1" <-> "OD2" Residue "D ASP 543": "OD1" <-> "OD2" Residue "D ASP 544": "OD1" <-> "OD2" Residue "D GLU 560": "OE1" <-> "OE2" Residue "D ARG 580": "NH1" <-> "NH2" Residue "D GLU 601": "OE1" <-> "OE2" Residue "D ASP 604": "OD1" <-> "OD2" Residue "D ARG 606": "NH1" <-> "NH2" Residue "D GLU 615": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17596 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4270 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 15, 'TRANS': 501} Chain: "B" Number of atoms: 4270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4270 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 15, 'TRANS': 501} Chain: "C" Number of atoms: 4270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4270 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 15, 'TRANS': 501} Chain: "D" Number of atoms: 4270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4270 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 15, 'TRANS': 501} Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Unusual residues: {'CPL': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'CPL:plan-4': 6, 'CPL:plan-3': 6, 'CPL:plan-2': 3, 'CPL:plan-1': 3} Unresolved non-hydrogen planarities: 68 Chain: "B" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Unusual residues: {'CPL': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'CPL:plan-4': 6, 'CPL:plan-3': 6, 'CPL:plan-2': 3, 'CPL:plan-1': 3} Unresolved non-hydrogen planarities: 68 Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Unusual residues: {'CPL': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'CPL:plan-4': 6, 'CPL:plan-3': 6, 'CPL:plan-2': 3, 'CPL:plan-1': 3} Unresolved non-hydrogen planarities: 68 Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Unusual residues: {'CPL': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'CPL:plan-4': 6, 'CPL:plan-3': 6, 'CPL:plan-2': 3, 'CPL:plan-1': 3} Unresolved non-hydrogen planarities: 68 Time building chain proxies: 9.29, per 1000 atoms: 0.53 Number of scatterers: 17596 At special positions: 0 Unit cell: (130.31, 130.31, 136.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 12 15.00 O 3096 8.00 N 2872 7.00 C 11520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 172 " distance=2.02 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 172 " distance=2.02 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 172 " distance=2.02 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 172 " distance=2.02 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: 7.43 Conformation dependent library (CDL) restraints added in 3.2 seconds 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3912 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 12 sheets defined 52.2% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.51 Creating SS restraints... Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 119 through 144 removed outlier: 5.129A pdb=" N ILE A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 223 Processing helix chain 'A' and resid 237 through 246 Processing helix chain 'A' and resid 250 through 257 removed outlier: 3.919A pdb=" N LEU A 257 " --> pdb=" O ASP A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 264 No H-bonds generated for 'chain 'A' and resid 261 through 264' Processing helix chain 'A' and resid 277 through 285 removed outlier: 4.172A pdb=" N ASN A 282 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 298 Processing helix chain 'A' and resid 304 through 334 Processing helix chain 'A' and resid 359 through 374 Processing helix chain 'A' and resid 386 through 437 removed outlier: 3.573A pdb=" N MET A 417 " --> pdb=" O MET A 413 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N SER A 418 " --> pdb=" O ILE A 414 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ALA A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TRP A 421 " --> pdb=" O MET A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 457 Processing helix chain 'A' and resid 465 through 470 Processing helix chain 'A' and resid 473 through 488 removed outlier: 3.600A pdb=" N HIS A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLU A 486 " --> pdb=" O GLN A 482 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N THR A 487 " --> pdb=" O VAL A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 506 Processing helix chain 'A' and resid 592 through 600 Processing helix chain 'A' and resid 603 through 618 Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 119 through 144 removed outlier: 5.129A pdb=" N ILE B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 223 Processing helix chain 'B' and resid 237 through 246 Processing helix chain 'B' and resid 250 through 257 removed outlier: 3.919A pdb=" N LEU B 257 " --> pdb=" O ASP B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 264 No H-bonds generated for 'chain 'B' and resid 261 through 264' Processing helix chain 'B' and resid 277 through 285 removed outlier: 4.172A pdb=" N ASN B 282 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG B 283 " --> pdb=" O ARG B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 298 Processing helix chain 'B' and resid 304 through 334 Processing helix chain 'B' and resid 359 through 374 Processing helix chain 'B' and resid 386 through 437 removed outlier: 3.573A pdb=" N MET B 417 " --> pdb=" O MET B 413 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER B 418 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA B 419 " --> pdb=" O SER B 415 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ALA B 420 " --> pdb=" O ASN B 416 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TRP B 421 " --> pdb=" O MET B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 457 Processing helix chain 'B' and resid 465 through 470 Processing helix chain 'B' and resid 473 through 488 removed outlier: 3.600A pdb=" N HIS B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLU B 486 " --> pdb=" O GLN B 482 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N THR B 487 " --> pdb=" O VAL B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 506 Processing helix chain 'B' and resid 592 through 600 Processing helix chain 'B' and resid 603 through 618 Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 119 through 144 removed outlier: 5.129A pdb=" N ILE C 140 " --> pdb=" O LEU C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 223 Processing helix chain 'C' and resid 237 through 246 Processing helix chain 'C' and resid 250 through 257 removed outlier: 3.920A pdb=" N LEU C 257 " --> pdb=" O ASP C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 264 No H-bonds generated for 'chain 'C' and resid 261 through 264' Processing helix chain 'C' and resid 277 through 285 removed outlier: 4.172A pdb=" N ASN C 282 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG C 283 " --> pdb=" O ARG C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 298 Processing helix chain 'C' and resid 304 through 334 Processing helix chain 'C' and resid 359 through 374 Processing helix chain 'C' and resid 386 through 437 removed outlier: 3.573A pdb=" N MET C 417 " --> pdb=" O MET C 413 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER C 418 " --> pdb=" O ILE C 414 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ALA C 420 " --> pdb=" O ASN C 416 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TRP C 421 " --> pdb=" O MET C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 457 Processing helix chain 'C' and resid 465 through 470 Processing helix chain 'C' and resid 473 through 488 removed outlier: 3.601A pdb=" N HIS C 484 " --> pdb=" O ALA C 480 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLU C 486 " --> pdb=" O GLN C 482 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N THR C 487 " --> pdb=" O VAL C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 506 Processing helix chain 'C' and resid 592 through 600 Processing helix chain 'C' and resid 603 through 618 Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 119 through 144 removed outlier: 5.129A pdb=" N ILE D 140 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 223 Processing helix chain 'D' and resid 237 through 246 Processing helix chain 'D' and resid 250 through 257 removed outlier: 3.919A pdb=" N LEU D 257 " --> pdb=" O ASP D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 264 No H-bonds generated for 'chain 'D' and resid 261 through 264' Processing helix chain 'D' and resid 277 through 285 removed outlier: 4.172A pdb=" N ASN D 282 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG D 283 " --> pdb=" O ARG D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 298 Processing helix chain 'D' and resid 304 through 334 Processing helix chain 'D' and resid 359 through 374 Processing helix chain 'D' and resid 386 through 437 removed outlier: 3.573A pdb=" N MET D 417 " --> pdb=" O MET D 413 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER D 418 " --> pdb=" O ILE D 414 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA D 419 " --> pdb=" O SER D 415 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ALA D 420 " --> pdb=" O ASN D 416 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TRP D 421 " --> pdb=" O MET D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 457 Processing helix chain 'D' and resid 465 through 470 Processing helix chain 'D' and resid 473 through 488 removed outlier: 3.599A pdb=" N HIS D 484 " --> pdb=" O ALA D 480 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLU D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N THR D 487 " --> pdb=" O VAL D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 506 Processing helix chain 'D' and resid 592 through 600 Processing helix chain 'D' and resid 603 through 618 Processing sheet with id= A, first strand: chain 'A' and resid 185 through 188 removed outlier: 3.534A pdb=" N ASN A 161 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 166 " --> pdb=" O ASN A 161 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 511 through 514 removed outlier: 6.021A pdb=" N PHE A 588 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N VAL A 533 " --> pdb=" O PHE A 588 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU A 590 " --> pdb=" O TYR A 531 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N TYR A 531 " --> pdb=" O LEU A 590 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 538 through 541 removed outlier: 3.517A pdb=" N VAL A 541 " --> pdb=" O ASN A 578 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASN A 578 " --> pdb=" O VAL A 541 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 185 through 188 removed outlier: 3.535A pdb=" N ASN B 161 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER B 166 " --> pdb=" O ASN B 161 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 511 through 514 removed outlier: 6.021A pdb=" N PHE B 588 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N VAL B 533 " --> pdb=" O PHE B 588 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU B 590 " --> pdb=" O TYR B 531 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N TYR B 531 " --> pdb=" O LEU B 590 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 538 through 541 removed outlier: 3.517A pdb=" N VAL B 541 " --> pdb=" O ASN B 578 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASN B 578 " --> pdb=" O VAL B 541 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 185 through 188 removed outlier: 3.534A pdb=" N ASN C 161 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER C 166 " --> pdb=" O ASN C 161 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 511 through 514 removed outlier: 6.021A pdb=" N PHE C 588 " --> pdb=" O VAL C 533 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N VAL C 533 " --> pdb=" O PHE C 588 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU C 590 " --> pdb=" O TYR C 531 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N TYR C 531 " --> pdb=" O LEU C 590 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 538 through 541 removed outlier: 3.518A pdb=" N VAL C 541 " --> pdb=" O ASN C 578 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASN C 578 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 185 through 188 removed outlier: 3.534A pdb=" N ASN D 161 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER D 166 " --> pdb=" O ASN D 161 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 511 through 514 removed outlier: 6.021A pdb=" N PHE D 588 " --> pdb=" O VAL D 533 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N VAL D 533 " --> pdb=" O PHE D 588 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU D 590 " --> pdb=" O TYR D 531 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N TYR D 531 " --> pdb=" O LEU D 590 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 538 through 541 removed outlier: 3.517A pdb=" N VAL D 541 " --> pdb=" O ASN D 578 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASN D 578 " --> pdb=" O VAL D 541 " (cutoff:3.500A) 828 hydrogen bonds defined for protein. 2412 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: 5.04 Time building geometry restraints manager: 7.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2672 1.30 - 1.43: 5063 1.43 - 1.56: 10069 1.56 - 1.68: 32 1.68 - 1.81: 156 Bond restraints: 17992 Sorted by residual: bond pdb=" C11 CPL C1806 " pdb=" O3 CPL C1806 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C11 CPL A 805 " pdb=" O3 CPL A 805 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C11 CPL B1806 " pdb=" O3 CPL B1806 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C31 CPL D1801 " pdb=" O2 CPL D1801 " ideal model delta sigma weight residual 1.332 1.404 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C31 CPL B1801 " pdb=" O2 CPL B1801 " ideal model delta sigma weight residual 1.332 1.404 -0.072 2.00e-02 2.50e+03 1.28e+01 ... (remaining 17987 not shown) Histogram of bond angle deviations from ideal: 97.69 - 104.98: 244 104.98 - 112.26: 8457 112.26 - 119.55: 6988 119.55 - 126.83: 8314 126.83 - 134.12: 297 Bond angle restraints: 24300 Sorted by residual: angle pdb=" O3P CPL C1801 " pdb=" P CPL C1801 " pdb=" O4P CPL C1801 " ideal model delta sigma weight residual 93.29 112.57 -19.28 3.00e+00 1.11e-01 4.13e+01 angle pdb=" O3P CPL B1801 " pdb=" P CPL B1801 " pdb=" O4P CPL B1801 " ideal model delta sigma weight residual 93.29 112.57 -19.28 3.00e+00 1.11e-01 4.13e+01 angle pdb=" O3P CPL D1801 " pdb=" P CPL D1801 " pdb=" O4P CPL D1801 " ideal model delta sigma weight residual 93.29 112.56 -19.27 3.00e+00 1.11e-01 4.13e+01 angle pdb=" O3P CPL A 806 " pdb=" P CPL A 806 " pdb=" O4P CPL A 806 " ideal model delta sigma weight residual 93.29 112.53 -19.24 3.00e+00 1.11e-01 4.11e+01 angle pdb=" O3P CPL C1806 " pdb=" P CPL C1806 " pdb=" O4P CPL C1806 " ideal model delta sigma weight residual 93.29 109.99 -16.70 3.00e+00 1.11e-01 3.10e+01 ... (remaining 24295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.39: 10384 35.39 - 70.77: 300 70.77 - 106.16: 40 106.16 - 141.54: 8 141.54 - 176.93: 8 Dihedral angle restraints: 10740 sinusoidal: 4640 harmonic: 6100 Sorted by residual: dihedral pdb=" CA LYS C 469 " pdb=" C LYS C 469 " pdb=" N VAL C 470 " pdb=" CA VAL C 470 " ideal model delta harmonic sigma weight residual 180.00 -155.08 -24.92 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA LYS D 469 " pdb=" C LYS D 469 " pdb=" N VAL D 470 " pdb=" CA VAL D 470 " ideal model delta harmonic sigma weight residual -180.00 -155.11 -24.89 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA LYS B 469 " pdb=" C LYS B 469 " pdb=" N VAL B 470 " pdb=" CA VAL B 470 " ideal model delta harmonic sigma weight residual -180.00 -155.13 -24.87 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 10737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1926 0.060 - 0.121: 553 0.121 - 0.181: 99 0.181 - 0.241: 54 0.241 - 0.302: 12 Chirality restraints: 2644 Sorted by residual: chirality pdb=" CA PHE A 403 " pdb=" N PHE A 403 " pdb=" C PHE A 403 " pdb=" CB PHE A 403 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA PHE C 403 " pdb=" N PHE C 403 " pdb=" C PHE C 403 " pdb=" CB PHE C 403 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA PHE D 403 " pdb=" N PHE D 403 " pdb=" C PHE D 403 " pdb=" CB PHE D 403 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 2641 not shown) Planarity restraints: 2960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 150 " -0.051 5.00e-02 4.00e+02 7.72e-02 9.54e+00 pdb=" N PRO C 151 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO C 151 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 151 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 150 " 0.051 5.00e-02 4.00e+02 7.69e-02 9.47e+00 pdb=" N PRO A 151 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 151 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 151 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 150 " -0.051 5.00e-02 4.00e+02 7.69e-02 9.47e+00 pdb=" N PRO D 151 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO D 151 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 151 " -0.043 5.00e-02 4.00e+02 ... (remaining 2957 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.86: 6186 2.86 - 3.37: 15629 3.37 - 3.88: 29809 3.88 - 4.39: 33597 4.39 - 4.90: 57997 Nonbonded interactions: 143218 Sorted by model distance: nonbonded pdb=" OH TYR C 112 " pdb=" OE1 GLN C 114 " model vdw 2.355 2.440 nonbonded pdb=" OH TYR A 112 " pdb=" OE1 GLN A 114 " model vdw 2.355 2.440 nonbonded pdb=" OH TYR D 112 " pdb=" OE1 GLN D 114 " model vdw 2.356 2.440 nonbonded pdb=" OH TYR B 112 " pdb=" OE1 GLN B 114 " model vdw 2.356 2.440 nonbonded pdb=" O ASP D 453 " pdb=" OG1 THR D 457 " model vdw 2.368 2.440 ... (remaining 143213 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 103 through 619 or (resid 801 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C2 or name C3 or name C31 or name C32 o \ r name C33 or name C34 or name C4 or name C5 or name O11 or name O1P or name O2 \ or name O2P or name O3 or name O31 or name O3P or name O4P or name P )) or (resi \ d 802 through 803 and (name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19)) or (resid 804 through 805 and (name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C1 \ 9 or name C20 or name C21 or name C22 or name C23)) or (resid 806 and (name C1 o \ r name C11 or name C12 or name C13 or name C14 or name C2 or name C3 or name C31 \ or name C32 or name C33 or name C34 or name O11 or name O1P or name O2 or name \ O2P or name O3 or name O31 or name O3P or name O4P or name P )))) selection = (chain 'B' and (resid 103 through 619 or resid 1801 or (resid 1802 through 1803 \ and (name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or nam \ e C18 or name C19)) or (resid 1804 through 1805 and (name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or \ name C21 or name C22 or name C23)) or (resid 1806 and (name C1 or name C11 or n \ ame C12 or name C13 or name C14 or name C2 or name C3 or name C31 or name C32 or \ name C33 or name C34 or name O11 or name O1P or name O2 or name O2P or name O3 \ or name O31 or name O3P or name O4P or name P )))) selection = (chain 'C' and (resid 103 through 619 or resid 1801 or (resid 1802 through 1803 \ and (name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or nam \ e C18 or name C19)) or (resid 1804 through 1805 and (name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or \ name C21 or name C22 or name C23)) or (resid 1806 and (name C1 or name C11 or n \ ame C12 or name C13 or name C14 or name C2 or name C3 or name C31 or name C32 or \ name C33 or name C34 or name O11 or name O1P or name O2 or name O2P or name O3 \ or name O31 or name O3P or name O4P or name P )))) selection = (chain 'D' and (resid 103 through 619 or resid 1801 or (resid 1802 through 1803 \ and (name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or nam \ e C18 or name C19)) or (resid 1804 through 1805 and (name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or \ name C21 or name C22 or name C23)) or (resid 1806 and (name C1 or name C11 or n \ ame C12 or name C13 or name C14 or name C2 or name C3 or name C31 or name C32 or \ name C33 or name C34 or name O11 or name O1P or name O2 or name O2P or name O3 \ or name O31 or name O3P or name O4P or name P )))) } 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: 1.480 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: 6.560 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 49.180 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 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 0.103 17992 Z= 0.607 Angle : 1.325 19.278 24300 Z= 0.649 Chirality : 0.065 0.302 2644 Planarity : 0.009 0.077 2960 Dihedral : 18.631 176.927 6816 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.28 % Allowed : 6.62 % Favored : 92.09 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.58 (0.12), residues: 2060 helix: -3.59 (0.08), residues: 1204 sheet: -1.96 (0.32), residues: 192 loop : -1.70 (0.18), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP D 266 HIS 0.006 0.002 HIS C 199 PHE 0.019 0.003 PHE D 328 TYR 0.029 0.003 TYR D 363 ARG 0.011 0.001 ARG C 614 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 296 time to evaluate : 1.899 Fit side-chains revert: symmetry clash REVERT: A 112 TYR cc_start: 0.8466 (t80) cc_final: 0.7997 (t80) REVERT: A 270 TYR cc_start: 0.7490 (m-80) cc_final: 0.7161 (m-80) REVERT: A 397 MET cc_start: 0.7596 (mmm) cc_final: 0.7249 (mtm) REVERT: A 426 ASN cc_start: 0.8321 (m110) cc_final: 0.7894 (m110) REVERT: A 478 GLU cc_start: 0.8256 (tp30) cc_final: 0.7925 (tp30) REVERT: A 537 ARG cc_start: 0.7976 (ttm-80) cc_final: 0.7636 (ttm110) REVERT: B 112 TYR cc_start: 0.8455 (t80) cc_final: 0.7934 (t80) REVERT: B 270 TYR cc_start: 0.7479 (m-80) cc_final: 0.7158 (m-80) REVERT: B 397 MET cc_start: 0.7596 (mmm) cc_final: 0.7214 (mtm) REVERT: B 426 ASN cc_start: 0.8310 (m110) cc_final: 0.7934 (m110) REVERT: B 478 GLU cc_start: 0.8233 (tp30) cc_final: 0.7889 (tp30) REVERT: B 537 ARG cc_start: 0.8005 (ttm-80) cc_final: 0.7264 (ttm110) REVERT: C 112 TYR cc_start: 0.8454 (t80) cc_final: 0.7957 (t80) REVERT: C 270 TYR cc_start: 0.7506 (m-80) cc_final: 0.7180 (m-80) REVERT: C 397 MET cc_start: 0.7598 (mmm) cc_final: 0.7238 (mtm) REVERT: C 426 ASN cc_start: 0.8259 (m110) cc_final: 0.7884 (m110) REVERT: C 478 GLU cc_start: 0.8212 (tp30) cc_final: 0.7873 (tp30) REVERT: C 537 ARG cc_start: 0.7961 (ttm-80) cc_final: 0.7274 (ttm110) REVERT: D 270 TYR cc_start: 0.7511 (m-80) cc_final: 0.7182 (m-80) REVERT: D 397 MET cc_start: 0.7554 (mmm) cc_final: 0.7207 (mtm) REVERT: D 426 ASN cc_start: 0.8324 (m110) cc_final: 0.7917 (m110) REVERT: D 478 GLU cc_start: 0.8232 (tp30) cc_final: 0.7905 (tp30) REVERT: D 537 ARG cc_start: 0.7933 (ttm-80) cc_final: 0.7606 (ttm110) REVERT: D 558 PHE cc_start: 0.8292 (p90) cc_final: 0.7988 (p90) outliers start: 24 outliers final: 4 residues processed: 316 average time/residue: 0.3153 time to fit residues: 145.9287 Evaluate side-chains 221 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 217 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 205 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 3.9990 chunk 154 optimal weight: 0.0370 chunk 85 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 119 optimal weight: 0.6980 chunk 185 optimal weight: 0.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 GLN ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 GLN A 578 ASN B 199 HIS B 426 ASN B 460 GLN ** B 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 GLN B 578 ASN C 426 ASN C 460 GLN ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 578 ASN D 246 GLN ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 GLN ** D 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 GLN D 578 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17992 Z= 0.146 Angle : 0.502 7.239 24300 Z= 0.261 Chirality : 0.039 0.136 2644 Planarity : 0.005 0.037 2960 Dihedral : 15.620 172.312 2728 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.64 % Allowed : 8.81 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.16), residues: 2060 helix: -0.78 (0.13), residues: 1164 sheet: -0.93 (0.36), residues: 192 loop : -1.03 (0.20), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 329 HIS 0.001 0.001 HIS C 321 PHE 0.014 0.001 PHE B 558 TYR 0.010 0.001 TYR D 363 ARG 0.003 0.000 ARG B 438 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 248 time to evaluate : 1.919 Fit side-chains REVERT: A 270 TYR cc_start: 0.7560 (m-80) cc_final: 0.7263 (m-80) REVERT: A 426 ASN cc_start: 0.7949 (m110) cc_final: 0.7540 (m110) REVERT: A 478 GLU cc_start: 0.8113 (tp30) cc_final: 0.7764 (tp30) REVERT: A 481 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7810 (mmm) REVERT: A 537 ARG cc_start: 0.7845 (ttm-80) cc_final: 0.7577 (ttm110) REVERT: A 589 VAL cc_start: 0.8784 (t) cc_final: 0.8445 (m) REVERT: B 270 TYR cc_start: 0.7560 (m-80) cc_final: 0.7267 (m-80) REVERT: B 426 ASN cc_start: 0.7895 (m-40) cc_final: 0.7464 (m110) REVERT: B 453 ASP cc_start: 0.7251 (m-30) cc_final: 0.6868 (m-30) REVERT: B 478 GLU cc_start: 0.8180 (tp30) cc_final: 0.7855 (tp30) REVERT: C 270 TYR cc_start: 0.7551 (m-80) cc_final: 0.7260 (m-80) REVERT: C 426 ASN cc_start: 0.7828 (m-40) cc_final: 0.7444 (m110) REVERT: C 478 GLU cc_start: 0.8136 (tp30) cc_final: 0.7762 (tp30) REVERT: C 481 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7821 (mmm) REVERT: C 589 VAL cc_start: 0.8903 (t) cc_final: 0.8519 (m) REVERT: D 262 TYR cc_start: 0.8519 (m-80) cc_final: 0.8150 (m-80) REVERT: D 270 TYR cc_start: 0.7543 (m-80) cc_final: 0.7234 (m-80) REVERT: D 426 ASN cc_start: 0.8052 (m110) cc_final: 0.7638 (m110) REVERT: D 478 GLU cc_start: 0.8165 (tp30) cc_final: 0.7814 (tp30) REVERT: D 481 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7776 (mmm) REVERT: D 537 ARG cc_start: 0.7897 (ttm-80) cc_final: 0.7614 (ttm110) outliers start: 12 outliers final: 5 residues processed: 257 average time/residue: 0.3011 time to fit residues: 116.7814 Evaluate side-chains 227 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 219 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 481 MET Chi-restraints excluded: chain D residue 542 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 20.0000 chunk 57 optimal weight: 0.0050 chunk 154 optimal weight: 1.9990 chunk 126 optimal weight: 0.0980 chunk 51 optimal weight: 20.0000 chunk 185 optimal weight: 0.8980 chunk 200 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 184 optimal weight: 0.6980 chunk 63 optimal weight: 7.9990 chunk 148 optimal weight: 4.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 ASN ** D 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 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 : 0.002 0.022 17992 Z= 0.130 Angle : 0.451 7.173 24300 Z= 0.232 Chirality : 0.038 0.139 2644 Planarity : 0.003 0.034 2960 Dihedral : 13.071 155.033 2724 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.96 % Allowed : 11.75 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.18), residues: 2060 helix: 0.51 (0.15), residues: 1164 sheet: -0.40 (0.36), residues: 184 loop : -0.60 (0.21), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 124 HIS 0.002 0.000 HIS B 199 PHE 0.016 0.001 PHE D 558 TYR 0.010 0.001 TYR A 365 ARG 0.002 0.000 ARG D 447 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 240 time to evaluate : 1.998 Fit side-chains REVERT: A 426 ASN cc_start: 0.7857 (m-40) cc_final: 0.7415 (m110) REVERT: A 436 GLU cc_start: 0.7723 (tp30) cc_final: 0.7472 (tp30) REVERT: A 438 ARG cc_start: 0.7102 (mpt180) cc_final: 0.6893 (mpt180) REVERT: A 453 ASP cc_start: 0.7185 (m-30) cc_final: 0.6737 (m-30) REVERT: A 478 GLU cc_start: 0.8180 (tp30) cc_final: 0.7806 (tp30) REVERT: A 481 MET cc_start: 0.8198 (mmt) cc_final: 0.7875 (mmm) REVERT: A 589 VAL cc_start: 0.8698 (t) cc_final: 0.8404 (m) REVERT: B 416 ASN cc_start: 0.8653 (t0) cc_final: 0.8433 (t0) REVERT: B 426 ASN cc_start: 0.7822 (m-40) cc_final: 0.7395 (m110) REVERT: B 436 GLU cc_start: 0.7876 (tp30) cc_final: 0.7617 (tp30) REVERT: B 453 ASP cc_start: 0.7191 (m-30) cc_final: 0.6720 (m-30) REVERT: B 478 GLU cc_start: 0.8243 (tp30) cc_final: 0.7875 (tp30) REVERT: C 426 ASN cc_start: 0.7767 (m-40) cc_final: 0.7347 (m110) REVERT: C 436 GLU cc_start: 0.7736 (tp30) cc_final: 0.7516 (tp30) REVERT: C 438 ARG cc_start: 0.7021 (mpt180) cc_final: 0.6801 (mpt180) REVERT: C 453 ASP cc_start: 0.7218 (m-30) cc_final: 0.6839 (m-30) REVERT: C 478 GLU cc_start: 0.8155 (tp30) cc_final: 0.7912 (tp30) REVERT: C 481 MET cc_start: 0.8166 (mmt) cc_final: 0.7850 (mmm) REVERT: C 589 VAL cc_start: 0.8751 (t) cc_final: 0.8431 (m) REVERT: D 262 TYR cc_start: 0.8479 (m-80) cc_final: 0.8162 (m-80) REVERT: D 426 ASN cc_start: 0.7881 (m-40) cc_final: 0.7441 (m110) REVERT: D 478 GLU cc_start: 0.8165 (tp30) cc_final: 0.7775 (tp30) REVERT: D 537 ARG cc_start: 0.7797 (ttm-80) cc_final: 0.7567 (ttm110) outliers start: 18 outliers final: 9 residues processed: 253 average time/residue: 0.2931 time to fit residues: 111.9280 Evaluate side-chains 221 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 212 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 460 GLN Chi-restraints excluded: chain D residue 542 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 20 optimal weight: 0.0980 chunk 88 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 186 optimal weight: 8.9990 chunk 197 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 176 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 GLN ** D 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17992 Z= 0.346 Angle : 0.538 7.136 24300 Z= 0.277 Chirality : 0.042 0.157 2644 Planarity : 0.004 0.031 2960 Dihedral : 12.936 144.211 2724 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.66 % Allowed : 11.32 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.18), residues: 2060 helix: 0.62 (0.15), residues: 1192 sheet: -0.37 (0.35), residues: 192 loop : -0.42 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 596 HIS 0.003 0.001 HIS B 199 PHE 0.027 0.002 PHE B 558 TYR 0.012 0.001 TYR B 363 ARG 0.002 0.000 ARG C 201 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 222 time to evaluate : 2.285 Fit side-chains REVERT: A 426 ASN cc_start: 0.7959 (m-40) cc_final: 0.7537 (m110) REVERT: A 453 ASP cc_start: 0.7307 (m-30) cc_final: 0.6858 (m-30) REVERT: A 478 GLU cc_start: 0.8250 (tp30) cc_final: 0.7853 (tp30) REVERT: A 481 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7788 (mmm) REVERT: A 589 VAL cc_start: 0.8750 (t) cc_final: 0.8512 (m) REVERT: B 416 ASN cc_start: 0.8751 (t0) cc_final: 0.8538 (t0) REVERT: B 426 ASN cc_start: 0.7973 (m-40) cc_final: 0.7528 (m110) REVERT: B 436 GLU cc_start: 0.7907 (tp30) cc_final: 0.7609 (tp30) REVERT: B 453 ASP cc_start: 0.7330 (m-30) cc_final: 0.6866 (m-30) REVERT: B 478 GLU cc_start: 0.8279 (tp30) cc_final: 0.7962 (tp30) REVERT: B 482 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8321 (tt0) REVERT: C 426 ASN cc_start: 0.7938 (m-40) cc_final: 0.7523 (m110) REVERT: C 453 ASP cc_start: 0.7309 (m-30) cc_final: 0.6858 (m-30) REVERT: C 478 GLU cc_start: 0.8256 (tp30) cc_final: 0.8026 (tp30) REVERT: C 481 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7844 (mmm) REVERT: C 589 VAL cc_start: 0.8805 (t) cc_final: 0.8560 (m) REVERT: D 262 TYR cc_start: 0.8611 (m-80) cc_final: 0.8211 (m-80) REVERT: D 423 GLU cc_start: 0.8184 (tp30) cc_final: 0.7968 (tp30) REVERT: D 426 ASN cc_start: 0.8062 (m-40) cc_final: 0.7630 (m110) REVERT: D 437 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7722 (mp) REVERT: D 453 ASP cc_start: 0.7285 (m-30) cc_final: 0.6800 (m-30) REVERT: D 478 GLU cc_start: 0.8216 (tp30) cc_final: 0.7809 (tp30) REVERT: D 481 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7795 (mmm) REVERT: D 537 ARG cc_start: 0.7887 (ttm-80) cc_final: 0.7592 (ttm110) REVERT: D 589 VAL cc_start: 0.8655 (t) cc_final: 0.8412 (m) outliers start: 31 outliers final: 15 residues processed: 241 average time/residue: 0.2817 time to fit residues: 105.1288 Evaluate side-chains 234 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 214 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 482 GLN Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 481 MET Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 542 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 146 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 100 optimal weight: 8.9990 chunk 176 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 GLN C 199 HIS ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 HIS D 230 GLN ** D 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 17992 Z= 0.154 Angle : 0.460 8.878 24300 Z= 0.235 Chirality : 0.039 0.140 2644 Planarity : 0.003 0.030 2960 Dihedral : 11.698 129.335 2724 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.39 % Allowed : 11.59 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.19), residues: 2060 helix: 1.07 (0.16), residues: 1184 sheet: -0.03 (0.35), residues: 192 loop : -0.16 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 124 HIS 0.002 0.000 HIS B 199 PHE 0.032 0.001 PHE A 558 TYR 0.010 0.001 TYR A 365 ARG 0.003 0.000 ARG D 438 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 224 time to evaluate : 1.975 Fit side-chains revert: symmetry clash REVERT: A 426 ASN cc_start: 0.7825 (m-40) cc_final: 0.7405 (m110) REVERT: A 438 ARG cc_start: 0.7353 (mpt180) cc_final: 0.7015 (mpt180) REVERT: A 453 ASP cc_start: 0.7211 (m-30) cc_final: 0.6698 (m-30) REVERT: A 478 GLU cc_start: 0.8232 (tp30) cc_final: 0.7819 (tp30) REVERT: A 481 MET cc_start: 0.8184 (mmt) cc_final: 0.7869 (mmm) REVERT: A 554 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7832 (tm-30) REVERT: A 589 VAL cc_start: 0.8669 (t) cc_final: 0.8425 (m) REVERT: B 262 TYR cc_start: 0.8591 (m-80) cc_final: 0.8218 (m-80) REVERT: B 416 ASN cc_start: 0.8725 (t0) cc_final: 0.8493 (t0) REVERT: B 423 GLU cc_start: 0.8044 (tp30) cc_final: 0.7812 (tp30) REVERT: B 426 ASN cc_start: 0.7852 (m-40) cc_final: 0.7448 (m110) REVERT: B 436 GLU cc_start: 0.7862 (tp30) cc_final: 0.7532 (tp30) REVERT: B 438 ARG cc_start: 0.7237 (mpt180) cc_final: 0.6813 (mpt180) REVERT: B 453 ASP cc_start: 0.7210 (m-30) cc_final: 0.6672 (m-30) REVERT: B 478 GLU cc_start: 0.8254 (tp30) cc_final: 0.7873 (tp30) REVERT: C 262 TYR cc_start: 0.8592 (m-80) cc_final: 0.8216 (m-80) REVERT: C 423 GLU cc_start: 0.8063 (tp30) cc_final: 0.7850 (tp30) REVERT: C 426 ASN cc_start: 0.7813 (m-40) cc_final: 0.7417 (m110) REVERT: C 438 ARG cc_start: 0.7297 (mpt180) cc_final: 0.6980 (mpt180) REVERT: C 453 ASP cc_start: 0.7246 (m-30) cc_final: 0.6803 (m-30) REVERT: C 478 GLU cc_start: 0.8228 (tp30) cc_final: 0.7993 (tp30) REVERT: C 481 MET cc_start: 0.8177 (mmt) cc_final: 0.7875 (mmm) REVERT: C 589 VAL cc_start: 0.8731 (t) cc_final: 0.8495 (m) REVERT: D 262 TYR cc_start: 0.8563 (m-80) cc_final: 0.8169 (m-80) REVERT: D 426 ASN cc_start: 0.7840 (m-40) cc_final: 0.7432 (m110) REVERT: D 437 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7642 (mp) REVERT: D 453 ASP cc_start: 0.7215 (m-30) cc_final: 0.6673 (m-30) REVERT: D 478 GLU cc_start: 0.8192 (tp30) cc_final: 0.7779 (tp30) REVERT: D 481 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7811 (mmm) outliers start: 26 outliers final: 20 residues processed: 243 average time/residue: 0.2771 time to fit residues: 103.9954 Evaluate side-chains 242 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 220 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 542 ASP Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 481 MET Chi-restraints excluded: chain D residue 542 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 0.0060 chunk 177 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 197 optimal weight: 20.0000 chunk 163 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 16 optimal weight: 0.0070 chunk 65 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.4020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 GLN ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17992 Z= 0.214 Angle : 0.482 8.543 24300 Z= 0.248 Chirality : 0.039 0.138 2644 Planarity : 0.003 0.028 2960 Dihedral : 11.015 106.834 2724 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.98 % Allowed : 11.27 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.19), residues: 2060 helix: 1.15 (0.16), residues: 1180 sheet: 0.06 (0.37), residues: 172 loop : -0.09 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 456 HIS 0.003 0.001 HIS D 199 PHE 0.026 0.001 PHE A 558 TYR 0.011 0.001 TYR C 363 ARG 0.003 0.000 ARG D 438 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 228 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.8620 (m-80) cc_final: 0.8243 (m-80) REVERT: A 423 GLU cc_start: 0.8118 (tp30) cc_final: 0.7912 (tp30) REVERT: A 426 ASN cc_start: 0.7887 (m-40) cc_final: 0.7461 (m110) REVERT: A 438 ARG cc_start: 0.7350 (mpt180) cc_final: 0.6991 (mpt180) REVERT: A 453 ASP cc_start: 0.7220 (m-30) cc_final: 0.6652 (m-30) REVERT: A 478 GLU cc_start: 0.8266 (tp30) cc_final: 0.7861 (tp30) REVERT: A 481 MET cc_start: 0.8190 (mmt) cc_final: 0.7877 (mmm) REVERT: A 552 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8592 (mp) REVERT: A 554 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7870 (tm-30) REVERT: A 589 VAL cc_start: 0.8696 (t) cc_final: 0.8455 (m) REVERT: B 262 TYR cc_start: 0.8609 (m-80) cc_final: 0.8204 (m-80) REVERT: B 426 ASN cc_start: 0.7881 (m-40) cc_final: 0.7475 (m110) REVERT: B 436 GLU cc_start: 0.7861 (tp30) cc_final: 0.7512 (tp30) REVERT: B 453 ASP cc_start: 0.7230 (m-30) cc_final: 0.6698 (m-30) REVERT: B 478 GLU cc_start: 0.8268 (tp30) cc_final: 0.7883 (tp30) REVERT: C 262 TYR cc_start: 0.8604 (m-80) cc_final: 0.8196 (m-80) REVERT: C 426 ASN cc_start: 0.7862 (m-40) cc_final: 0.7448 (m110) REVERT: C 438 ARG cc_start: 0.7321 (mpt180) cc_final: 0.6953 (mpt180) REVERT: C 453 ASP cc_start: 0.7258 (m-30) cc_final: 0.6751 (m-30) REVERT: C 478 GLU cc_start: 0.8258 (tp30) cc_final: 0.8030 (tp30) REVERT: C 481 MET cc_start: 0.8176 (mmt) cc_final: 0.7882 (mmm) REVERT: C 554 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7876 (tm-30) REVERT: C 589 VAL cc_start: 0.8760 (t) cc_final: 0.8537 (m) REVERT: D 262 TYR cc_start: 0.8604 (m-80) cc_final: 0.8224 (m-80) REVERT: D 426 ASN cc_start: 0.8008 (m-40) cc_final: 0.7559 (m110) REVERT: D 428 MET cc_start: 0.8128 (tpp) cc_final: 0.7684 (ttt) REVERT: D 453 ASP cc_start: 0.7198 (m-30) cc_final: 0.6575 (m-30) REVERT: D 478 GLU cc_start: 0.8235 (tp30) cc_final: 0.8000 (tp30) REVERT: D 481 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7799 (mmm) outliers start: 37 outliers final: 28 residues processed: 255 average time/residue: 0.2678 time to fit residues: 105.7273 Evaluate side-chains 249 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 219 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 542 ASP Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 481 MET Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 542 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 chunk 111 optimal weight: 0.0670 chunk 166 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 196 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 90 optimal weight: 20.0000 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17992 Z= 0.191 Angle : 0.484 8.563 24300 Z= 0.243 Chirality : 0.039 0.136 2644 Planarity : 0.003 0.029 2960 Dihedral : 9.378 57.901 2724 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.82 % Allowed : 11.91 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.19), residues: 2060 helix: 1.28 (0.16), residues: 1180 sheet: 0.17 (0.37), residues: 172 loop : -0.03 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 456 HIS 0.002 0.001 HIS B 199 PHE 0.024 0.001 PHE A 558 TYR 0.010 0.001 TYR C 365 ARG 0.002 0.000 ARG B 438 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 220 time to evaluate : 1.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.8612 (m-80) cc_final: 0.8218 (m-80) REVERT: A 426 ASN cc_start: 0.7869 (m-40) cc_final: 0.7449 (m110) REVERT: A 438 ARG cc_start: 0.7374 (mpt180) cc_final: 0.7048 (mpt180) REVERT: A 453 ASP cc_start: 0.7221 (m-30) cc_final: 0.6606 (m-30) REVERT: A 478 GLU cc_start: 0.8271 (tp30) cc_final: 0.7900 (tp30) REVERT: A 481 MET cc_start: 0.8220 (mmt) cc_final: 0.7899 (mmm) REVERT: A 552 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8567 (mp) REVERT: A 554 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7873 (tm-30) REVERT: A 589 VAL cc_start: 0.8690 (t) cc_final: 0.8458 (m) REVERT: B 262 TYR cc_start: 0.8600 (m-80) cc_final: 0.8220 (m-80) REVERT: B 426 ASN cc_start: 0.7938 (m-40) cc_final: 0.7501 (m110) REVERT: B 436 GLU cc_start: 0.7866 (tp30) cc_final: 0.7526 (tp30) REVERT: B 438 ARG cc_start: 0.7242 (mpt180) cc_final: 0.7024 (mpt180) REVERT: B 453 ASP cc_start: 0.7209 (m-30) cc_final: 0.6669 (m-30) REVERT: B 478 GLU cc_start: 0.8269 (tp30) cc_final: 0.7879 (tp30) REVERT: C 262 TYR cc_start: 0.8601 (m-80) cc_final: 0.8221 (m-80) REVERT: C 426 ASN cc_start: 0.7873 (m-40) cc_final: 0.7465 (m110) REVERT: C 438 ARG cc_start: 0.7272 (mpt180) cc_final: 0.6884 (mpt180) REVERT: C 453 ASP cc_start: 0.7209 (m-30) cc_final: 0.6649 (m-30) REVERT: C 478 GLU cc_start: 0.8240 (tp30) cc_final: 0.7823 (tp30) REVERT: C 481 MET cc_start: 0.8209 (mmt) cc_final: 0.7919 (mmm) REVERT: C 554 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7881 (tm-30) REVERT: C 589 VAL cc_start: 0.8704 (t) cc_final: 0.8479 (m) REVERT: D 262 TYR cc_start: 0.8610 (m-80) cc_final: 0.8240 (m-80) REVERT: D 426 ASN cc_start: 0.7987 (m-40) cc_final: 0.7540 (m110) REVERT: D 428 MET cc_start: 0.8147 (tpp) cc_final: 0.7671 (ttt) REVERT: D 478 GLU cc_start: 0.8265 (tp30) cc_final: 0.8027 (tp30) REVERT: D 481 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7861 (mmm) outliers start: 34 outliers final: 28 residues processed: 248 average time/residue: 0.2719 time to fit residues: 103.7611 Evaluate side-chains 248 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 218 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 542 ASP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 460 GLN Chi-restraints excluded: chain D residue 481 MET Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 542 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 chunk 125 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 154 optimal weight: 0.6980 chunk 178 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17992 Z= 0.165 Angle : 0.466 8.693 24300 Z= 0.235 Chirality : 0.039 0.139 2644 Planarity : 0.003 0.030 2960 Dihedral : 8.761 58.007 2724 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.55 % Allowed : 12.39 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.19), residues: 2060 helix: 1.39 (0.16), residues: 1180 sheet: 0.27 (0.38), residues: 172 loop : 0.03 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 124 HIS 0.002 0.001 HIS B 199 PHE 0.021 0.001 PHE A 558 TYR 0.010 0.001 TYR B 365 ARG 0.002 0.000 ARG B 438 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 223 time to evaluate : 2.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.8587 (m-80) cc_final: 0.8219 (m-80) REVERT: A 426 ASN cc_start: 0.7900 (m-40) cc_final: 0.7444 (m110) REVERT: A 438 ARG cc_start: 0.7368 (mpt180) cc_final: 0.7014 (mpt180) REVERT: A 453 ASP cc_start: 0.7200 (m-30) cc_final: 0.6639 (m-30) REVERT: A 478 GLU cc_start: 0.8256 (tp30) cc_final: 0.7894 (tp30) REVERT: A 481 MET cc_start: 0.8162 (mmt) cc_final: 0.7890 (mmm) REVERT: A 552 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8578 (mp) REVERT: A 554 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7885 (tm-30) REVERT: A 589 VAL cc_start: 0.8634 (t) cc_final: 0.8407 (m) REVERT: B 262 TYR cc_start: 0.8590 (m-80) cc_final: 0.8231 (m-80) REVERT: B 426 ASN cc_start: 0.7928 (m-40) cc_final: 0.7492 (m110) REVERT: B 436 GLU cc_start: 0.7877 (tp30) cc_final: 0.7541 (tp30) REVERT: B 438 ARG cc_start: 0.7247 (mpt180) cc_final: 0.6952 (mpt180) REVERT: B 478 GLU cc_start: 0.8269 (tp30) cc_final: 0.7890 (tp30) REVERT: B 537 ARG cc_start: 0.7826 (ttm-80) cc_final: 0.7521 (ttm110) REVERT: C 262 TYR cc_start: 0.8593 (m-80) cc_final: 0.8228 (m-80) REVERT: C 426 ASN cc_start: 0.7929 (m-40) cc_final: 0.7475 (m110) REVERT: C 438 ARG cc_start: 0.7238 (mpt180) cc_final: 0.6833 (mpt180) REVERT: C 478 GLU cc_start: 0.8244 (tp30) cc_final: 0.7829 (tp30) REVERT: C 481 MET cc_start: 0.8189 (mmt) cc_final: 0.7913 (mmm) REVERT: C 554 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7881 (tm-30) REVERT: C 589 VAL cc_start: 0.8664 (t) cc_final: 0.8451 (m) REVERT: D 202 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7419 (mmt) REVERT: D 262 TYR cc_start: 0.8605 (m-80) cc_final: 0.8238 (m-80) REVERT: D 426 ASN cc_start: 0.7966 (m-40) cc_final: 0.7535 (m110) REVERT: D 428 MET cc_start: 0.8149 (tpp) cc_final: 0.7696 (ttt) REVERT: D 478 GLU cc_start: 0.8208 (tp30) cc_final: 0.7973 (tp30) REVERT: D 481 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7881 (mmm) outliers start: 29 outliers final: 23 residues processed: 246 average time/residue: 0.2812 time to fit residues: 106.5162 Evaluate side-chains 244 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 218 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 481 MET Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 542 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 4.9990 chunk 171 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 79 optimal weight: 0.0470 chunk 143 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 173 optimal weight: 0.8980 chunk 182 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17992 Z= 0.135 Angle : 0.456 8.712 24300 Z= 0.229 Chirality : 0.038 0.152 2644 Planarity : 0.003 0.031 2960 Dihedral : 8.291 59.830 2724 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.34 % Allowed : 13.09 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.19), residues: 2060 helix: 1.49 (0.16), residues: 1188 sheet: 0.34 (0.39), residues: 172 loop : 0.17 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 124 HIS 0.001 0.000 HIS B 199 PHE 0.011 0.001 PHE C 328 TYR 0.009 0.001 TYR A 365 ARG 0.002 0.000 ARG C 438 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 232 time to evaluate : 2.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.8540 (m-80) cc_final: 0.8151 (m-80) REVERT: A 426 ASN cc_start: 0.7897 (m-40) cc_final: 0.7465 (m110) REVERT: A 438 ARG cc_start: 0.7302 (mpt180) cc_final: 0.6931 (mpt180) REVERT: A 478 GLU cc_start: 0.8283 (tp30) cc_final: 0.7919 (tp30) REVERT: A 481 MET cc_start: 0.8127 (mmt) cc_final: 0.7867 (mmm) REVERT: A 537 ARG cc_start: 0.7758 (ttm-80) cc_final: 0.7459 (ttm110) REVERT: A 554 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7909 (tm-30) REVERT: A 589 VAL cc_start: 0.8578 (t) cc_final: 0.8295 (m) REVERT: B 202 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.7340 (mmt) REVERT: B 262 TYR cc_start: 0.8551 (m-80) cc_final: 0.8209 (m-80) REVERT: B 426 ASN cc_start: 0.7860 (m-40) cc_final: 0.7435 (m110) REVERT: B 436 GLU cc_start: 0.7836 (tp30) cc_final: 0.7520 (tp30) REVERT: B 478 GLU cc_start: 0.8252 (tp30) cc_final: 0.7879 (tp30) REVERT: B 537 ARG cc_start: 0.7797 (ttm-80) cc_final: 0.7511 (ttm110) REVERT: C 262 TYR cc_start: 0.8551 (m-80) cc_final: 0.8206 (m-80) REVERT: C 426 ASN cc_start: 0.7881 (m-40) cc_final: 0.7445 (m110) REVERT: C 438 ARG cc_start: 0.7231 (mpt180) cc_final: 0.6835 (mpt180) REVERT: C 478 GLU cc_start: 0.8237 (tp30) cc_final: 0.7824 (tp30) REVERT: C 481 MET cc_start: 0.8157 (mmt) cc_final: 0.7884 (mmm) REVERT: C 554 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7909 (tm-30) REVERT: C 589 VAL cc_start: 0.8609 (t) cc_final: 0.8400 (m) REVERT: D 202 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.7392 (mmt) REVERT: D 262 TYR cc_start: 0.8562 (m-80) cc_final: 0.8220 (m-80) REVERT: D 426 ASN cc_start: 0.7938 (m-40) cc_final: 0.7502 (m110) REVERT: D 428 MET cc_start: 0.8131 (tpp) cc_final: 0.7687 (ttt) REVERT: D 478 GLU cc_start: 0.8197 (tp30) cc_final: 0.7767 (tp30) REVERT: D 481 MET cc_start: 0.8149 (mmt) cc_final: 0.7858 (mmm) outliers start: 25 outliers final: 22 residues processed: 252 average time/residue: 0.2884 time to fit residues: 111.4566 Evaluate side-chains 248 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 224 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 460 GLN Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 542 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 chunk 203 optimal weight: 7.9990 chunk 187 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 16 optimal weight: 0.0970 chunk 125 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17992 Z= 0.233 Angle : 0.503 8.534 24300 Z= 0.252 Chirality : 0.040 0.156 2644 Planarity : 0.003 0.031 2960 Dihedral : 8.699 53.309 2724 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.34 % Allowed : 13.25 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.19), residues: 2060 helix: 1.36 (0.15), residues: 1192 sheet: 0.28 (0.39), residues: 172 loop : 0.17 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 596 HIS 0.003 0.001 HIS B 199 PHE 0.014 0.001 PHE A 328 TYR 0.011 0.001 TYR C 363 ARG 0.002 0.000 ARG B 201 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 215 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.8614 (m-80) cc_final: 0.8175 (m-80) REVERT: A 426 ASN cc_start: 0.7972 (m-40) cc_final: 0.7512 (m110) REVERT: A 438 ARG cc_start: 0.7303 (mpt180) cc_final: 0.6926 (mpt180) REVERT: A 478 GLU cc_start: 0.8284 (tp30) cc_final: 0.7918 (tp30) REVERT: A 481 MET cc_start: 0.8125 (mmt) cc_final: 0.7853 (mmm) REVERT: A 554 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7892 (tm-30) REVERT: A 589 VAL cc_start: 0.8585 (t) cc_final: 0.8315 (m) REVERT: B 262 TYR cc_start: 0.8606 (m-80) cc_final: 0.8169 (m-80) REVERT: B 426 ASN cc_start: 0.7958 (m-40) cc_final: 0.7508 (m110) REVERT: B 436 GLU cc_start: 0.7855 (tp30) cc_final: 0.7524 (tp30) REVERT: B 438 ARG cc_start: 0.7290 (mpt180) cc_final: 0.6934 (mpt180) REVERT: B 478 GLU cc_start: 0.8271 (tp30) cc_final: 0.7889 (tp30) REVERT: C 262 TYR cc_start: 0.8609 (m-80) cc_final: 0.8219 (m-80) REVERT: C 426 ASN cc_start: 0.7962 (m-40) cc_final: 0.7508 (m110) REVERT: C 438 ARG cc_start: 0.7240 (mpt180) cc_final: 0.6812 (mpt180) REVERT: C 478 GLU cc_start: 0.8237 (tp30) cc_final: 0.7821 (tp30) REVERT: C 481 MET cc_start: 0.8156 (mmt) cc_final: 0.7884 (mmm) REVERT: C 554 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7859 (tm-30) REVERT: C 589 VAL cc_start: 0.8650 (t) cc_final: 0.8447 (m) REVERT: D 262 TYR cc_start: 0.8618 (m-80) cc_final: 0.8231 (m-80) REVERT: D 426 ASN cc_start: 0.8054 (m-40) cc_final: 0.7619 (m110) REVERT: D 428 MET cc_start: 0.8144 (tpp) cc_final: 0.7687 (ttt) REVERT: D 478 GLU cc_start: 0.8259 (tp30) cc_final: 0.8021 (tp30) REVERT: D 481 MET cc_start: 0.8168 (mmt) cc_final: 0.7878 (mmm) outliers start: 25 outliers final: 25 residues processed: 236 average time/residue: 0.2674 time to fit residues: 98.0460 Evaluate side-chains 239 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 214 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 460 GLN Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 542 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 149 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 44 optimal weight: 0.0370 chunk 162 optimal weight: 0.6980 chunk 67 optimal weight: 0.0030 chunk 166 optimal weight: 4.9990 chunk 20 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 overall best weight: 0.5870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** 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 = 0.4090 r_free = 0.4090 target = 0.177846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.121656 restraints weight = 20347.517| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.13 r_work: 0.3256 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 17992 Z= 0.130 Angle : 0.462 8.425 24300 Z= 0.230 Chirality : 0.038 0.153 2644 Planarity : 0.003 0.030 2960 Dihedral : 8.126 53.735 2724 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.23 % Allowed : 13.46 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.19), residues: 2060 helix: 1.55 (0.16), residues: 1188 sheet: 0.13 (0.44), residues: 132 loop : 0.27 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 124 HIS 0.001 0.000 HIS B 199 PHE 0.012 0.001 PHE C 328 TYR 0.009 0.001 TYR A 365 ARG 0.001 0.000 ARG B 614 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3875.22 seconds wall clock time: 71 minutes 4.70 seconds (4264.70 seconds total)