Starting phenix.real_space_refine on Wed Feb 14 19:30:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx3_24723/02_2024/7rx3_24723_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx3_24723/02_2024/7rx3_24723.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx3_24723/02_2024/7rx3_24723.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx3_24723/02_2024/7rx3_24723.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx3_24723/02_2024/7rx3_24723_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx3_24723/02_2024/7rx3_24723_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 14 5.49 5 S 38 5.16 5 C 6684 2.51 5 N 1600 2.21 5 O 1794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 17": "OD1" <-> "OD2" Residue "B GLU 31": "OE1" <-> "OE2" Residue "B GLU 42": "OE1" <-> "OE2" Residue "B PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B GLU 121": "OE1" <-> "OE2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "B GLU 225": "OE1" <-> "OE2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B GLU 232": "OE1" <-> "OE2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 250": "NH1" <-> "NH2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B GLU 350": "OE1" <-> "OE2" Residue "B ARG 391": "NH1" <-> "NH2" Residue "B ARG 425": "NH1" <-> "NH2" Residue "B ARG 492": "NH1" <-> "NH2" Residue "B ARG 496": "NH1" <-> "NH2" Residue "B GLU 502": "OE1" <-> "OE2" Residue "B ASP 507": "OD1" <-> "OD2" Residue "B PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 625": "NH1" <-> "NH2" Residue "B ARG 641": "NH1" <-> "NH2" Residue "B GLU 646": "OE1" <-> "OE2" Residue "B ARG 647": "NH1" <-> "NH2" Residue "B ARG 651": "NH1" <-> "NH2" Residue "B GLU 703": "OE1" <-> "OE2" Residue "B ARG 710": "NH1" <-> "NH2" Residue "A ASP 17": "OD1" <-> "OD2" Residue "A GLU 31": "OE1" <-> "OE2" Residue "A GLU 42": "OE1" <-> "OE2" Residue "A PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 65": "NH1" <-> "NH2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ARG 250": "NH1" <-> "NH2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A GLU 350": "OE1" <-> "OE2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A GLU 502": "OE1" <-> "OE2" Residue "A ASP 507": "OD1" <-> "OD2" Residue "A PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 625": "NH1" <-> "NH2" Residue "A ARG 641": "NH1" <-> "NH2" Residue "A GLU 646": "OE1" <-> "OE2" Residue "A ARG 647": "NH1" <-> "NH2" Residue "A ARG 651": "NH1" <-> "NH2" Residue "A GLU 703": "OE1" <-> "OE2" Residue "A ARG 710": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10130 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4786 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 25, 'TRANS': 565} Chain breaks: 6 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "A" Number of atoms: 4786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4786 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 25, 'TRANS': 565} Chain breaks: 6 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 279 Unusual residues: {'PGW': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PGW:plan-3': 4} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 279 Unusual residues: {'PGW': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PGW:plan-3': 4} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 5.71, per 1000 atoms: 0.56 Number of scatterers: 10130 At special positions: 0 Unit cell: (128.26, 96.46, 101.76, 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 38 16.00 P 14 15.00 O 1794 8.00 N 1600 7.00 C 6684 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.91 Conformation dependent library (CDL) restraints added in 1.7 seconds 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2260 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 2 sheets defined 65.1% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'B' and resid 29 through 45 removed outlier: 3.753A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS B 34 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 86 Processing helix chain 'B' and resid 105 through 116 removed outlier: 3.997A pdb=" N ILE B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 157 removed outlier: 3.832A pdb=" N TRP B 155 " --> pdb=" O CYS B 151 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B 156 " --> pdb=" O MET B 152 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LYS B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 171 Processing helix chain 'B' and resid 176 through 203 removed outlier: 3.741A pdb=" N TYR B 180 " --> pdb=" O HIS B 176 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N MET B 192 " --> pdb=" O PHE B 188 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N PHE B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Proline residue: B 194 - end of helix removed outlier: 3.678A pdb=" N TRP B 202 " --> pdb=" O GLY B 198 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 203 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 237 removed outlier: 3.878A pdb=" N ILE B 224 " --> pdb=" O CYS B 220 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 310 removed outlier: 3.543A pdb=" N LEU B 281 " --> pdb=" O MET B 277 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU B 282 " --> pdb=" O TYR B 278 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N GLN B 283 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N VAL B 284 " --> pdb=" O GLN B 280 " (cutoff:3.500A) Proline residue: B 285 - end of helix Processing helix chain 'B' and resid 318 through 321 No H-bonds generated for 'chain 'B' and resid 318 through 321' Processing helix chain 'B' and resid 323 through 349 Proline residue: B 333 - end of helix Processing helix chain 'B' and resid 355 through 374 Processing helix chain 'B' and resid 376 through 382 removed outlier: 4.040A pdb=" N THR B 381 " --> pdb=" O PRO B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 396 Proline residue: B 394 - end of helix Processing helix chain 'B' and resid 423 through 434 Processing helix chain 'B' and resid 436 through 446 removed outlier: 3.820A pdb=" N GLY B 441 " --> pdb=" O ALA B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 502 removed outlier: 3.605A pdb=" N THR B 495 " --> pdb=" O ALA B 491 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN B 499 " --> pdb=" O THR B 495 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU B 502 " --> pdb=" O ARG B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 523 removed outlier: 4.567A pdb=" N GLU B 514 " --> pdb=" O ASP B 510 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET B 515 " --> pdb=" O ASP B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 542 removed outlier: 3.667A pdb=" N ASN B 539 " --> pdb=" O SER B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 553 Processing helix chain 'B' and resid 569 through 591 removed outlier: 3.677A pdb=" N ILE B 582 " --> pdb=" O TRP B 578 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR B 589 " --> pdb=" O SER B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 632 removed outlier: 4.078A pdb=" N LEU B 612 " --> pdb=" O TRP B 608 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE B 623 " --> pdb=" O HIS B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 658 removed outlier: 3.948A pdb=" N GLU B 643 " --> pdb=" O ASN B 639 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 658 " --> pdb=" O TYR B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 707 No H-bonds generated for 'chain 'B' and resid 705 through 707' Processing helix chain 'B' and resid 713 through 726 Processing helix chain 'A' and resid 29 through 45 removed outlier: 3.753A pdb=" N ILE A 33 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS A 34 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 86 Processing helix chain 'A' and resid 105 through 116 removed outlier: 3.997A pdb=" N ILE A 111 " --> pdb=" O ARG A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 157 removed outlier: 3.833A pdb=" N TRP A 155 " --> pdb=" O CYS A 151 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 156 " --> pdb=" O MET A 152 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LYS A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 171 Processing helix chain 'A' and resid 176 through 203 removed outlier: 3.741A pdb=" N TYR A 180 " --> pdb=" O HIS A 176 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N MET A 192 " --> pdb=" O PHE A 188 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N PHE A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Proline residue: A 194 - end of helix removed outlier: 3.678A pdb=" N TRP A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 203 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 237 removed outlier: 3.879A pdb=" N ILE A 224 " --> pdb=" O CYS A 220 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 310 removed outlier: 3.544A pdb=" N LEU A 281 " --> pdb=" O MET A 277 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU A 282 " --> pdb=" O TYR A 278 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N GLN A 283 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N VAL A 284 " --> pdb=" O GLN A 280 " (cutoff:3.500A) Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 318 through 321 No H-bonds generated for 'chain 'A' and resid 318 through 321' Processing helix chain 'A' and resid 323 through 349 Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 355 through 374 Processing helix chain 'A' and resid 376 through 382 removed outlier: 4.041A pdb=" N THR A 381 " --> pdb=" O PRO A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 396 Proline residue: A 394 - end of helix Processing helix chain 'A' and resid 423 through 434 Processing helix chain 'A' and resid 436 through 446 removed outlier: 3.821A pdb=" N GLY A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 502 removed outlier: 3.605A pdb=" N THR A 495 " --> pdb=" O ALA A 491 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN A 499 " --> pdb=" O THR A 495 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 523 removed outlier: 4.567A pdb=" N GLU A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET A 515 " --> pdb=" O ASP A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 542 removed outlier: 3.668A pdb=" N ASN A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 553 Processing helix chain 'A' and resid 569 through 591 removed outlier: 3.676A pdb=" N ILE A 582 " --> pdb=" O TRP A 578 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 589 " --> pdb=" O SER A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 632 removed outlier: 4.078A pdb=" N LEU A 612 " --> pdb=" O TRP A 608 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 623 " --> pdb=" O HIS A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 658 removed outlier: 3.948A pdb=" N GLU A 643 " --> pdb=" O ASN A 639 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 658 " --> pdb=" O TYR A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 707 No H-bonds generated for 'chain 'A' and resid 705 through 707' Processing helix chain 'A' and resid 713 through 726 Processing sheet with id= A, first strand: chain 'B' and resid 139 through 141 removed outlier: 3.784A pdb=" N PHE B 61 " --> pdb=" O ARG B 53 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG B 53 " --> pdb=" O PHE B 61 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 139 through 141 removed outlier: 3.784A pdb=" N PHE A 61 " --> pdb=" O ARG A 53 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG A 53 " --> pdb=" O PHE A 61 " (cutoff:3.500A) 508 hydrogen bonds defined for protein. 1518 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: 2.67 Time building geometry restraints manager: 4.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1512 1.30 - 1.43: 2940 1.43 - 1.56: 5818 1.56 - 1.69: 34 1.69 - 1.82: 56 Bond restraints: 10360 Sorted by residual: bond pdb=" C1 PGW B 807 " pdb=" O01 PGW B 807 " ideal model delta sigma weight residual 1.332 1.424 -0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" C1 PGW A 902 " pdb=" O01 PGW A 902 " ideal model delta sigma weight residual 1.332 1.424 -0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" C1 PGW B 803 " pdb=" O01 PGW B 803 " ideal model delta sigma weight residual 1.332 1.424 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C1 PGW A 906 " pdb=" O01 PGW A 906 " ideal model delta sigma weight residual 1.332 1.424 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C1 PGW A 901 " pdb=" O01 PGW A 901 " ideal model delta sigma weight residual 1.332 1.423 -0.091 2.00e-02 2.50e+03 2.07e+01 ... (remaining 10355 not shown) Histogram of bond angle deviations from ideal: 100.16 - 107.00: 288 107.00 - 113.84: 5835 113.84 - 120.69: 4774 120.69 - 127.53: 2939 127.53 - 134.37: 118 Bond angle restraints: 13954 Sorted by residual: angle pdb=" C LYS B 158 " pdb=" N THR B 159 " pdb=" CA THR B 159 " ideal model delta sigma weight residual 121.54 132.59 -11.05 1.91e+00 2.74e-01 3.34e+01 angle pdb=" C LYS A 158 " pdb=" N THR A 159 " pdb=" CA THR A 159 " ideal model delta sigma weight residual 121.54 132.57 -11.03 1.91e+00 2.74e-01 3.33e+01 angle pdb=" N VAL A 508 " pdb=" CA VAL A 508 " pdb=" C VAL A 508 " ideal model delta sigma weight residual 112.96 107.84 5.12 1.00e+00 1.00e+00 2.62e+01 angle pdb=" N VAL B 508 " pdb=" CA VAL B 508 " pdb=" C VAL B 508 " ideal model delta sigma weight residual 112.96 107.87 5.09 1.00e+00 1.00e+00 2.59e+01 angle pdb=" C LEU A 331 " pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 120.24 123.42 -3.18 6.30e-01 2.52e+00 2.54e+01 ... (remaining 13949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.51: 5819 32.51 - 65.03: 321 65.03 - 97.54: 62 97.54 - 130.05: 16 130.05 - 162.56: 14 Dihedral angle restraints: 6232 sinusoidal: 2754 harmonic: 3478 Sorted by residual: dihedral pdb=" CA VAL B 117 " pdb=" C VAL B 117 " pdb=" N PRO B 118 " pdb=" CA PRO B 118 " ideal model delta harmonic sigma weight residual -180.00 -153.46 -26.54 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA VAL A 117 " pdb=" C VAL A 117 " pdb=" N PRO A 118 " pdb=" CA PRO A 118 " ideal model delta harmonic sigma weight residual -180.00 -153.46 -26.54 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" O01 PGW A 905 " pdb=" C01 PGW A 905 " pdb=" C02 PGW A 905 " pdb=" O03 PGW A 905 " ideal model delta sinusoidal sigma weight residual 59.30 -103.26 162.56 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 6229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1003 0.049 - 0.098: 376 0.098 - 0.147: 104 0.147 - 0.197: 29 0.197 - 0.246: 10 Chirality restraints: 1522 Sorted by residual: chirality pdb=" C02 PGW B 806 " pdb=" C01 PGW B 806 " pdb=" C03 PGW B 806 " pdb=" O01 PGW B 806 " both_signs ideal model delta sigma weight residual False 2.36 2.60 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" C02 PGW A 901 " pdb=" C01 PGW A 901 " pdb=" C03 PGW A 901 " pdb=" O01 PGW A 901 " both_signs ideal model delta sigma weight residual False 2.36 2.60 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB ILE B 332 " pdb=" CA ILE B 332 " pdb=" CG1 ILE B 332 " pdb=" CG2 ILE B 332 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1519 not shown) Planarity restraints: 1698 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 317 " 0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C LYS A 317 " -0.056 2.00e-02 2.50e+03 pdb=" O LYS A 317 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY A 318 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 317 " 0.016 2.00e-02 2.50e+03 3.22e-02 1.03e+01 pdb=" C LYS B 317 " -0.056 2.00e-02 2.50e+03 pdb=" O LYS B 317 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY B 318 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 422 " -0.050 5.00e-02 4.00e+02 7.60e-02 9.25e+00 pdb=" N PRO A 423 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 423 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 423 " -0.042 5.00e-02 4.00e+02 ... (remaining 1695 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 3232 2.84 - 3.36: 9047 3.36 - 3.87: 16308 3.87 - 4.39: 18541 4.39 - 4.90: 32696 Nonbonded interactions: 79824 Sorted by model distance: nonbonded pdb=" O SER B 420 " pdb=" OG SER B 420 " model vdw 2.327 2.440 nonbonded pdb=" O SER A 420 " pdb=" OG SER A 420 " model vdw 2.327 2.440 nonbonded pdb=" OH TYR A 589 " pdb=" O ILE A 605 " model vdw 2.350 2.440 nonbonded pdb=" OH TYR B 589 " pdb=" O ILE B 605 " model vdw 2.350 2.440 nonbonded pdb=" O SER A 207 " pdb=" OAE PGW A 905 " model vdw 2.359 2.440 ... (remaining 79819 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 11 through 728 or resid 901 or (resid 902 and (name C01 or \ name C02 or name C03 or name C15 or name C19 or name C2 or name C20 or name C21 \ or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name \ C3 or name C4 or name C5 or name O01 or name O02 or name O03 or name O04 or nam \ e O11)) or (resid 903 and (name C01 or name C02 or name C03 or name C1 or name C \ 19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C24 or nam \ e C25 or name C26 or name C27 or name C3 or name C4 or name C5 or name C6 or nam \ e C7 or name C8 or name C9 or name O01 or name O02 or name O03 or name O04 or na \ me O11 or name O12 or name O13 or name O14 or name P )) or (resid 904 and (name \ C01 or name C02 or name C03 or name C06 or name C07 or name C08 or name C1 or na \ me C10 or name C15 or name C16 or name C17 or name C19 or name C2 or name C20 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C2 \ 7 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 o \ r name O01 or name O02 or name O03 or name O04 or name O11 or name O12 or name O \ 13 or name O14 or name P )) or resid 905 through 906 or (resid 907 and (name C01 \ or name C02 or name C03 or name C06 or name C1 or name C10 or name C15 or name \ C16 or name C17 or name C19 or name C2 or name C20 or name C21 or name C22 or na \ me C23 or name C24 or name C25 or name C26 or name C27 or name C3 or name C4 or \ name C5 or name C6 or name C7 or name C8 or name C9 or name O01 or name O02 or n \ ame O03 or name O04 or name O11)) or (resid 908 and (name C01 or name C02 or nam \ e C03 or name C1 or name C19 or name C2 or name C20 or name C21 or name C22 or n \ ame C23 or name C24 or name C25 or name C26 or name C27 or name C3 or name C4 or \ name C5 or name C6 or name C7 or name O01 or name O02 or name O03 or name O04 o \ r name O11 or name O12 or name O13 or name O14 or name P )))) selection = (chain 'B' and (resid 11 through 728 or (resid 801 and (name C01 or name C02 or \ name C03 or name C1 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C \ 25 or name C26 or name C27 or name C28 or name C29 or name C3 or name C30 or nam \ e C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name O01 or name \ O02 or name O03 or name O04 or name O11 or name O12 or name O13 or name O14 or n \ ame P )) or (resid 802 and (name C01 or name C02 or name C03 or name C15 or name \ C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C24 or n \ ame C25 or name C26 or name C27 or name C3 or name C4 or name C5 or name O01 or \ name O02 or name O03 or name O04 or name O11)) or (resid 803 and (name C01 or na \ me C02 or name C03 or name C1 or name C19 or name C2 or name C20 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C3 \ or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name O01 or \ name O02 or name O03 or name O04 or name O11 or name O12 or name O13 or name O1 \ 4 or name P )) or (resid 804 and (name C01 or name C02 or name C03 or name C06 o \ r name C07 or name C08 or name C1 or name C10 or name C15 or name C16 or name C1 \ 7 or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name \ C24 or name C25 or name C26 or name C27 or name C3 or name C4 or name C5 or nam \ e C6 or name C7 or name C8 or name C9 or name O01 or name O02 or name O03 or nam \ e O04 or name O11 or name O12 or name O13 or name O14 or name P )) or (resid 805 \ and (name C01 or name C02 or name C03 or name C04 or name C05 or name C1 or nam \ e C15 or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or \ name C24 or name C25 or name C26 or name C27 or name C3 or name C4 or name C5 or \ name CAD or name O01 or name O02 or name O03 or name O04 or name O11 or name O1 \ 2 or name O13 or name O14 or name OAE or name OAF or name P )) or (resid 806 and \ (name C01 or name C02 or name C03 or name C1 or name C15 or name C19 or name C2 \ or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name \ C26 or name C27 or name C3 or name C4 or name C5 or name C6 or name C7 or name \ C8 or name C9 or name O01 or name O02 or name O03 or name O04 or name O11 or nam \ e O12 or name O13 or name O14 or name P )) or resid 807 or (resid 808 and (name \ C01 or name C02 or name C03 or name C1 or name C19 or name C2 or name C20 or nam \ e C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or \ name C3 or name C4 or name C5 or name C6 or name C7 or name O01 or name O02 or \ name O03 or name O04 or name O11 or name O12 or name O13 or name O14 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.580 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 28.870 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 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 0.092 10360 Z= 0.578 Angle : 1.375 11.750 13954 Z= 0.635 Chirality : 0.059 0.246 1522 Planarity : 0.008 0.076 1698 Dihedral : 22.826 162.563 3972 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.20 % Allowed : 8.27 % Favored : 91.54 % 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: -3.98 (0.19), residues: 1154 helix: -2.14 (0.13), residues: 800 sheet: -1.01 (0.71), residues: 44 loop : -3.82 (0.30), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 155 HIS 0.005 0.002 HIS A 619 PHE 0.016 0.002 PHE B 253 TYR 0.013 0.002 TYR A 24 ARG 0.003 0.001 ARG B 496 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 1.130 Fit side-chains REVERT: B 84 TRP cc_start: 0.7073 (m100) cc_final: 0.5199 (t60) REVERT: B 442 PHE cc_start: 0.7746 (t80) cc_final: 0.7439 (t80) REVERT: A 84 TRP cc_start: 0.6945 (m100) cc_final: 0.5172 (t60) REVERT: A 442 PHE cc_start: 0.7706 (t80) cc_final: 0.7368 (t80) outliers start: 2 outliers final: 0 residues processed: 99 average time/residue: 0.2333 time to fit residues: 32.6265 Evaluate side-chains 58 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.5980 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 68 optimal weight: 0.0050 chunk 107 optimal weight: 0.8980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 GLN A 280 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10360 Z= 0.162 Angle : 0.552 7.103 13954 Z= 0.275 Chirality : 0.039 0.142 1522 Planarity : 0.005 0.055 1698 Dihedral : 23.012 170.192 1768 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 1.77 % Allowed : 11.61 % Favored : 86.61 % 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: -1.40 (0.24), residues: 1154 helix: -0.05 (0.18), residues: 806 sheet: 0.16 (0.70), residues: 44 loop : -3.41 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 227 HIS 0.002 0.001 HIS B 619 PHE 0.013 0.001 PHE B 61 TYR 0.014 0.001 TYR A 278 ARG 0.004 0.000 ARG B 250 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 75 time to evaluate : 1.170 Fit side-chains REVERT: B 19 VAL cc_start: 0.8299 (OUTLIER) cc_final: 0.8025 (t) REVERT: B 84 TRP cc_start: 0.6954 (m100) cc_final: 0.5212 (t60) REVERT: B 442 PHE cc_start: 0.7618 (t80) cc_final: 0.7270 (t80) REVERT: A 84 TRP cc_start: 0.6969 (m100) cc_final: 0.5159 (t60) REVERT: A 277 MET cc_start: 0.7320 (ttp) cc_final: 0.7088 (mtp) REVERT: A 278 TYR cc_start: 0.7891 (m-80) cc_final: 0.7631 (m-10) outliers start: 18 outliers final: 7 residues processed: 88 average time/residue: 0.1917 time to fit residues: 25.3411 Evaluate side-chains 69 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 525 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 95 optimal weight: 0.0970 chunk 106 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10360 Z= 0.198 Angle : 0.550 8.015 13954 Z= 0.274 Chirality : 0.040 0.143 1522 Planarity : 0.005 0.061 1698 Dihedral : 21.360 174.440 1768 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.56 % Allowed : 12.30 % Favored : 85.14 % 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: -0.43 (0.26), residues: 1154 helix: 0.82 (0.19), residues: 796 sheet: 0.43 (0.71), residues: 44 loop : -3.35 (0.31), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 155 HIS 0.004 0.001 HIS B 619 PHE 0.015 0.001 PHE B 61 TYR 0.011 0.001 TYR B 589 ARG 0.002 0.000 ARG A 149 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 69 time to evaluate : 1.095 Fit side-chains REVERT: B 84 TRP cc_start: 0.6809 (m100) cc_final: 0.5024 (t60) REVERT: B 442 PHE cc_start: 0.7653 (t80) cc_final: 0.7350 (t80) REVERT: A 84 TRP cc_start: 0.6917 (m100) cc_final: 0.5116 (t60) REVERT: A 277 MET cc_start: 0.7285 (ttp) cc_final: 0.7069 (mtp) outliers start: 26 outliers final: 15 residues processed: 90 average time/residue: 0.1980 time to fit residues: 26.7501 Evaluate side-chains 76 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 61 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 525 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.0570 chunk 80 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 72 optimal weight: 0.0020 chunk 107 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 102 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 overall best weight: 0.4706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10360 Z= 0.133 Angle : 0.504 8.382 13954 Z= 0.251 Chirality : 0.038 0.142 1522 Planarity : 0.004 0.049 1698 Dihedral : 19.971 178.601 1768 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.26 % Allowed : 14.76 % Favored : 82.97 % 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: 0.17 (0.26), residues: 1154 helix: 1.33 (0.19), residues: 794 sheet: 0.57 (0.72), residues: 44 loop : -3.28 (0.31), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 155 HIS 0.002 0.001 HIS B 619 PHE 0.019 0.001 PHE A 442 TYR 0.008 0.001 TYR B 278 ARG 0.002 0.000 ARG B 168 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 72 time to evaluate : 1.086 Fit side-chains REVERT: B 84 TRP cc_start: 0.6549 (m100) cc_final: 0.4950 (t60) REVERT: B 442 PHE cc_start: 0.7638 (t80) cc_final: 0.7340 (t80) REVERT: A 84 TRP cc_start: 0.6530 (m100) cc_final: 0.4975 (t60) outliers start: 23 outliers final: 11 residues processed: 91 average time/residue: 0.1967 time to fit residues: 27.0146 Evaluate side-chains 79 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 576 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 28 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 283 GLN B 364 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10360 Z= 0.287 Angle : 0.579 8.208 13954 Z= 0.289 Chirality : 0.041 0.139 1522 Planarity : 0.004 0.045 1698 Dihedral : 19.875 174.093 1768 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.76 % Allowed : 14.57 % Favored : 82.68 % 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: 0.15 (0.26), residues: 1154 helix: 1.29 (0.19), residues: 804 sheet: 0.38 (0.75), residues: 44 loop : -3.32 (0.32), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 227 HIS 0.005 0.001 HIS A 619 PHE 0.020 0.002 PHE B 61 TYR 0.013 0.001 TYR B 589 ARG 0.002 0.000 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 73 time to evaluate : 1.190 Fit side-chains REVERT: B 84 TRP cc_start: 0.6718 (m100) cc_final: 0.5028 (t60) REVERT: B 442 PHE cc_start: 0.7688 (t80) cc_final: 0.7398 (t80) REVERT: A 84 TRP cc_start: 0.6764 (m100) cc_final: 0.5041 (t60) outliers start: 28 outliers final: 21 residues processed: 98 average time/residue: 0.1847 time to fit residues: 27.9319 Evaluate side-chains 89 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 68 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 712 TRP Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 712 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.9980 chunk 102 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 283 GLN B 364 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10360 Z= 0.287 Angle : 0.579 8.096 13954 Z= 0.289 Chirality : 0.041 0.145 1522 Planarity : 0.004 0.048 1698 Dihedral : 19.258 167.910 1768 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 3.15 % Allowed : 14.86 % Favored : 81.99 % 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 (0.26), residues: 1154 helix: 1.32 (0.19), residues: 802 sheet: 0.24 (0.76), residues: 44 loop : -3.30 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 227 HIS 0.004 0.001 HIS A 619 PHE 0.018 0.001 PHE A 61 TYR 0.011 0.001 TYR B 589 ARG 0.002 0.000 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 73 time to evaluate : 1.265 Fit side-chains REVERT: B 84 TRP cc_start: 0.6856 (m100) cc_final: 0.5062 (t60) REVERT: B 442 PHE cc_start: 0.7723 (t80) cc_final: 0.7429 (t80) REVERT: A 84 TRP cc_start: 0.6948 (m100) cc_final: 0.5091 (t60) outliers start: 32 outliers final: 24 residues processed: 100 average time/residue: 0.1869 time to fit residues: 28.6299 Evaluate side-chains 94 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 70 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 253 PHE Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 364 GLN Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 712 TRP Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 712 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 0.0020 chunk 63 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10360 Z= 0.209 Angle : 0.547 7.869 13954 Z= 0.272 Chirality : 0.040 0.138 1522 Planarity : 0.004 0.043 1698 Dihedral : 18.615 166.515 1768 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.17 % Allowed : 16.24 % Favored : 81.59 % 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: 0.35 (0.26), residues: 1154 helix: 1.48 (0.19), residues: 800 sheet: 0.26 (0.76), residues: 44 loop : -3.27 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 227 HIS 0.004 0.001 HIS A 619 PHE 0.016 0.001 PHE A 61 TYR 0.009 0.001 TYR B 589 ARG 0.001 0.000 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 70 time to evaluate : 1.115 Fit side-chains REVERT: B 84 TRP cc_start: 0.6686 (m100) cc_final: 0.5061 (t60) REVERT: B 442 PHE cc_start: 0.7705 (t80) cc_final: 0.7396 (t80) REVERT: A 84 TRP cc_start: 0.6703 (m100) cc_final: 0.5040 (t60) outliers start: 22 outliers final: 17 residues processed: 91 average time/residue: 0.1884 time to fit residues: 26.1715 Evaluate side-chains 88 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 71 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 576 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10360 Z= 0.234 Angle : 0.554 7.891 13954 Z= 0.275 Chirality : 0.040 0.138 1522 Planarity : 0.004 0.044 1698 Dihedral : 18.003 163.786 1768 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.66 % Allowed : 15.65 % Favored : 81.69 % 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: 0.44 (0.26), residues: 1154 helix: 1.55 (0.19), residues: 800 sheet: 0.34 (0.78), residues: 44 loop : -3.27 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 227 HIS 0.004 0.001 HIS A 619 PHE 0.017 0.001 PHE A 61 TYR 0.010 0.001 TYR B 589 ARG 0.002 0.000 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 70 time to evaluate : 1.090 Fit side-chains REVERT: B 84 TRP cc_start: 0.6707 (m100) cc_final: 0.5075 (t60) REVERT: B 442 PHE cc_start: 0.7711 (t80) cc_final: 0.7405 (t80) REVERT: A 84 TRP cc_start: 0.6675 (m100) cc_final: 0.5038 (t60) outliers start: 27 outliers final: 22 residues processed: 93 average time/residue: 0.2017 time to fit residues: 28.5124 Evaluate side-chains 90 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 68 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 253 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 576 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 chunk 105 optimal weight: 0.0020 chunk 63 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10360 Z= 0.153 Angle : 0.513 7.331 13954 Z= 0.254 Chirality : 0.038 0.134 1522 Planarity : 0.004 0.043 1698 Dihedral : 17.153 164.635 1768 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 1.97 % Allowed : 16.14 % Favored : 81.89 % 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: 0.72 (0.26), residues: 1154 helix: 1.79 (0.19), residues: 798 sheet: 0.39 (0.76), residues: 44 loop : -3.22 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 155 HIS 0.003 0.001 HIS B 619 PHE 0.013 0.001 PHE B 61 TYR 0.006 0.001 TYR A 589 ARG 0.001 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 77 time to evaluate : 1.153 Fit side-chains REVERT: B 84 TRP cc_start: 0.6617 (m100) cc_final: 0.5009 (t60) REVERT: B 442 PHE cc_start: 0.7695 (t80) cc_final: 0.7395 (t80) REVERT: A 84 TRP cc_start: 0.6632 (m100) cc_final: 0.4989 (t60) outliers start: 20 outliers final: 18 residues processed: 96 average time/residue: 0.1900 time to fit residues: 27.6473 Evaluate side-chains 89 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 71 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 253 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 576 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 chunk 108 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 9 optimal weight: 0.1980 chunk 72 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10360 Z= 0.173 Angle : 0.523 7.338 13954 Z= 0.259 Chirality : 0.039 0.133 1522 Planarity : 0.005 0.071 1698 Dihedral : 16.773 163.779 1768 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 1.67 % Allowed : 16.73 % Favored : 81.59 % 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: 0.82 (0.26), residues: 1154 helix: 1.88 (0.19), residues: 798 sheet: 0.29 (0.75), residues: 44 loop : -3.19 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 155 HIS 0.003 0.001 HIS B 619 PHE 0.013 0.001 PHE B 61 TYR 0.008 0.001 TYR B 589 ARG 0.001 0.000 ARG A 107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 73 time to evaluate : 1.078 Fit side-chains REVERT: B 84 TRP cc_start: 0.6594 (m100) cc_final: 0.4988 (t60) REVERT: B 442 PHE cc_start: 0.7704 (t80) cc_final: 0.7413 (t80) REVERT: A 84 TRP cc_start: 0.6611 (m100) cc_final: 0.4989 (t60) outliers start: 17 outliers final: 17 residues processed: 89 average time/residue: 0.1909 time to fit residues: 26.0793 Evaluate side-chains 88 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 71 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 576 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.0070 chunk 86 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 93 optimal weight: 0.3980 chunk 39 optimal weight: 7.9990 chunk 96 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.133841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.111934 restraints weight = 13216.183| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.19 r_work: 0.3190 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10360 Z= 0.150 Angle : 0.506 7.347 13954 Z= 0.251 Chirality : 0.038 0.132 1522 Planarity : 0.004 0.060 1698 Dihedral : 16.009 163.884 1768 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.67 % Allowed : 16.93 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.26), residues: 1154 helix: 1.96 (0.19), residues: 798 sheet: 0.37 (0.74), residues: 44 loop : -3.10 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 155 HIS 0.003 0.001 HIS B 619 PHE 0.012 0.001 PHE B 61 TYR 0.007 0.001 TYR A 589 ARG 0.001 0.000 ARG B 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1986.45 seconds wall clock time: 37 minutes 4.66 seconds (2224.66 seconds total)