Starting phenix.real_space_refine on Mon Aug 5 05:10:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9axa_43931/08_2024/9axa_43931.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9axa_43931/08_2024/9axa_43931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9axa_43931/08_2024/9axa_43931.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9axa_43931/08_2024/9axa_43931.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9axa_43931/08_2024/9axa_43931.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9axa_43931/08_2024/9axa_43931.cif" } resolution = 4.36 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 80 5.16 5 C 7902 2.51 5 N 2115 2.21 5 O 2318 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 385": "OE1" <-> "OE2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 152": "OD1" <-> "OD2" Residue "C TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 486": "OD1" <-> "OD2" Residue "C TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 17": "OE1" <-> "OE2" Residue "E TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 182": "OE1" <-> "OE2" Residue "E PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 14": "OE1" <-> "OE2" Residue "F ASP 104": "OD1" <-> "OD2" Residue "F ASP 139": "OD1" <-> "OD2" Residue "F TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 12421 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2207 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 12, 'TRANS': 260} Chain breaks: 2 Chain: "B" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2186 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 12, 'TRANS': 265} Chain breaks: 2 Chain: "C" Number of atoms: 2224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2224 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 12, 'TRANS': 262} Chain breaks: 2 Chain: "D" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2166 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 12, 'TRANS': 262} Chain breaks: 2 Chain: "E" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1785 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1785 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'A1AHE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'A1AHE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.25, per 1000 atoms: 0.58 Number of scatterers: 12421 At special positions: 0 Unit cell: (92.3355, 162.945, 101.388, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 80 16.00 P 2 15.00 F 4 9.00 O 2318 8.00 N 2115 7.00 C 7902 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: 4.78 Conformation dependent library (CDL) restraints added in 2.2 seconds 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2924 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 9 sheets defined 59.9% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 383 through 399 removed outlier: 3.865A pdb=" N LYS A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 435 Processing helix chain 'A' and resid 441 through 462 Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 526 through 542 removed outlier: 3.809A pdb=" N ASP A 530 " --> pdb=" O SER A 526 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 563 Processing helix chain 'A' and resid 569 through 573 removed outlier: 4.096A pdb=" N LYS A 572 " --> pdb=" O ASP A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 589 removed outlier: 3.623A pdb=" N VAL A 589 " --> pdb=" O VAL A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 611 Processing helix chain 'B' and resid 53 through 59 removed outlier: 3.698A pdb=" N LYS B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 150 through 159 removed outlier: 3.533A pdb=" N VAL B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 184 Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 231 through 237 Processing helix chain 'B' and resid 241 through 259 removed outlier: 4.057A pdb=" N ASP B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 331 through 342 Processing helix chain 'B' and resid 351 through 357 Processing helix chain 'B' and resid 358 through 367 Processing helix chain 'B' and resid 370 through 380 Processing helix chain 'C' and resid 383 through 399 removed outlier: 3.727A pdb=" N PHE C 387 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA C 389 " --> pdb=" O GLU C 385 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS C 399 " --> pdb=" O ALA C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 435 Processing helix chain 'C' and resid 441 through 462 Processing helix chain 'C' and resid 508 through 512 removed outlier: 3.829A pdb=" N TRP C 511 " --> pdb=" O SER C 508 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N MET C 512 " --> pdb=" O VAL C 509 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 508 through 512' Processing helix chain 'C' and resid 513 through 519 Processing helix chain 'C' and resid 526 through 544 removed outlier: 3.786A pdb=" N ASP C 530 " --> pdb=" O SER C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 563 removed outlier: 3.679A pdb=" N ILE C 557 " --> pdb=" O ASN C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 589 removed outlier: 3.503A pdb=" N VAL C 589 " --> pdb=" O VAL C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 612 removed outlier: 3.509A pdb=" N ILE C 602 " --> pdb=" O LEU C 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 66 No H-bonds generated for 'chain 'D' and resid 64 through 66' Processing helix chain 'D' and resid 104 through 116 Processing helix chain 'D' and resid 117 through 121 removed outlier: 3.687A pdb=" N CYS D 121 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 159 Processing helix chain 'D' and resid 162 through 185 Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 241 through 259 removed outlier: 4.147A pdb=" N ASP D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 331 through 342 Processing helix chain 'D' and resid 351 through 356 Processing helix chain 'D' and resid 358 through 367 Processing helix chain 'D' and resid 370 through 380 Processing helix chain 'E' and resid 2 through 16 Processing helix chain 'E' and resid 18 through 32 Processing helix chain 'E' and resid 37 through 70 Processing helix chain 'E' and resid 79 through 111 removed outlier: 5.850A pdb=" N ILE E 108 " --> pdb=" O ASP E 104 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LYS E 109 " --> pdb=" O SER E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 133 Processing helix chain 'E' and resid 137 through 162 removed outlier: 3.756A pdb=" N LYS E 141 " --> pdb=" O GLY E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 183 Processing helix chain 'E' and resid 186 through 204 Processing helix chain 'E' and resid 205 through 208 removed outlier: 3.713A pdb=" N LEU E 208 " --> pdb=" O LEU E 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 205 through 208' Processing helix chain 'E' and resid 209 through 231 removed outlier: 3.694A pdb=" N ILE E 219 " --> pdb=" O ASP E 215 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU E 222 " --> pdb=" O LEU E 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 15 Processing helix chain 'F' and resid 18 through 32 Processing helix chain 'F' and resid 37 through 70 Processing helix chain 'F' and resid 79 through 111 removed outlier: 5.893A pdb=" N ILE F 108 " --> pdb=" O ASP F 104 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LYS F 109 " --> pdb=" O SER F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 134 Processing helix chain 'F' and resid 137 through 162 Processing helix chain 'F' and resid 166 through 183 Processing helix chain 'F' and resid 186 through 205 Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 209 through 231 removed outlier: 4.131A pdb=" N ILE F 219 " --> pdb=" O ASP F 215 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU F 222 " --> pdb=" O LEU F 218 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 350 through 354 removed outlier: 6.364A pdb=" N LEU A 351 " --> pdb=" O LYS A 367 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS A 367 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR A 353 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 417 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 418 " --> pdb=" O MET A 412 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY A 410 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN A 422 " --> pdb=" O PHE A 408 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N PHE A 408 " --> pdb=" O GLN A 422 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 464 through 465 Processing sheet with id=AA3, first strand: chain 'A' and resid 474 through 477 Processing sheet with id=AA4, first strand: chain 'B' and resid 81 through 87 removed outlier: 3.670A pdb=" N LEU B 92 " --> pdb=" O HIS B 87 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 139 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY B 131 " --> pdb=" O CYS B 142 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLU B 144 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N PHE B 129 " --> pdb=" O GLU B 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 196 through 198 Processing sheet with id=AA6, first strand: chain 'C' and resid 365 through 367 removed outlier: 3.582A pdb=" N VAL C 372 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE C 419 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA C 418 " --> pdb=" O MET C 412 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET C 412 " --> pdb=" O ALA C 418 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY C 410 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N GLN C 422 " --> pdb=" O PHE C 408 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N PHE C 408 " --> pdb=" O GLN C 422 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 426 through 428 removed outlier: 3.901A pdb=" N SER C 427 " --> pdb=" O LEU C 476 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 68 through 73 removed outlier: 6.429A pdb=" N LYS D 70 " --> pdb=" O SER D 86 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N SER D 86 " --> pdb=" O LYS D 70 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS D 97 " --> pdb=" O ILE D 141 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE D 141 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE D 99 " --> pdb=" O ILE D 139 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE D 139 " --> pdb=" O ILE D 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 149 through 150 709 hydrogen bonds defined for protein. 2085 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: 3.82 Time building geometry restraints manager: 5.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3382 1.34 - 1.46: 2453 1.46 - 1.58: 6674 1.58 - 1.70: 12 1.70 - 1.82: 136 Bond restraints: 12657 Sorted by residual: bond pdb=" N GLU C 343 " pdb=" CA GLU C 343 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.39e+00 bond pdb=" N MET A 519 " pdb=" CA MET A 519 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.55e+00 bond pdb=" C21 A1AHE D 401 " pdb=" N22 A1AHE D 401 " ideal model delta sigma weight residual 1.306 1.357 -0.051 2.00e-02 2.50e+03 6.50e+00 bond pdb=" N MET D 219 " pdb=" CA MET D 219 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.31e+00 bond pdb=" C21 A1AHE B 401 " pdb=" N22 A1AHE B 401 " ideal model delta sigma weight residual 1.306 1.355 -0.049 2.00e-02 2.50e+03 6.03e+00 ... (remaining 12652 not shown) Histogram of bond angle deviations from ideal: 95.86 - 103.57: 164 103.57 - 111.28: 4830 111.28 - 118.99: 5449 118.99 - 126.70: 6451 126.70 - 134.41: 168 Bond angle restraints: 17062 Sorted by residual: angle pdb=" CB MET A 412 " pdb=" CG MET A 412 " pdb=" SD MET A 412 " ideal model delta sigma weight residual 112.70 124.57 -11.87 3.00e+00 1.11e-01 1.57e+01 angle pdb=" N GLU A 607 " pdb=" CA GLU A 607 " pdb=" CB GLU A 607 " ideal model delta sigma weight residual 110.28 116.38 -6.10 1.55e+00 4.16e-01 1.55e+01 angle pdb=" N GLN A 520 " pdb=" CA GLN A 520 " pdb=" C GLN A 520 " ideal model delta sigma weight residual 113.55 108.82 4.73 1.26e+00 6.30e-01 1.41e+01 angle pdb=" CA LYS F 124 " pdb=" CB LYS F 124 " pdb=" CG LYS F 124 " ideal model delta sigma weight residual 114.10 121.59 -7.49 2.00e+00 2.50e-01 1.40e+01 angle pdb=" C ALA E 16 " pdb=" N GLU E 17 " pdb=" CA GLU E 17 " ideal model delta sigma weight residual 122.61 128.45 -5.84 1.56e+00 4.11e-01 1.40e+01 ... (remaining 17057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 6981 17.81 - 35.61: 598 35.61 - 53.42: 117 53.42 - 71.22: 36 71.22 - 89.03: 9 Dihedral angle restraints: 7741 sinusoidal: 3224 harmonic: 4517 Sorted by residual: dihedral pdb=" CD ARG A 518 " pdb=" NE ARG A 518 " pdb=" CZ ARG A 518 " pdb=" NH1 ARG A 518 " ideal model delta sinusoidal sigma weight residual 0.00 40.09 -40.09 1 1.00e+01 1.00e-02 2.26e+01 dihedral pdb=" CA LEU C 510 " pdb=" C LEU C 510 " pdb=" N TRP C 511 " pdb=" CA TRP C 511 " ideal model delta harmonic sigma weight residual -180.00 -157.12 -22.88 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA ILE F 219 " pdb=" C ILE F 219 " pdb=" N MET F 220 " pdb=" CA MET F 220 " ideal model delta harmonic sigma weight residual 180.00 159.64 20.36 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 7738 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1312 0.050 - 0.100: 421 0.100 - 0.151: 121 0.151 - 0.201: 23 0.201 - 0.251: 5 Chirality restraints: 1882 Sorted by residual: chirality pdb=" CG LEU E 193 " pdb=" CB LEU E 193 " pdb=" CD1 LEU E 193 " pdb=" CD2 LEU E 193 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB THR E 98 " pdb=" CA THR E 98 " pdb=" OG1 THR E 98 " pdb=" CG2 THR E 98 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB VAL A 589 " pdb=" CA VAL A 589 " pdb=" CG1 VAL A 589 " pdb=" CG2 VAL A 589 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1879 not shown) Planarity restraints: 2171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 518 " 0.709 9.50e-02 1.11e+02 3.18e-01 6.15e+01 pdb=" NE ARG A 518 " -0.042 2.00e-02 2.50e+03 pdb=" CZ ARG A 518 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 518 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 518 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 230 " -0.033 2.00e-02 2.50e+03 3.53e-02 3.12e+01 pdb=" CG TRP E 230 " 0.093 2.00e-02 2.50e+03 pdb=" CD1 TRP E 230 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 TRP E 230 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 230 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP E 230 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 230 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 230 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 230 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP E 230 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 518 " -0.352 9.50e-02 1.11e+02 1.58e-01 1.52e+01 pdb=" NE ARG C 518 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG C 518 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG C 518 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 518 " -0.012 2.00e-02 2.50e+03 ... (remaining 2168 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2207 2.77 - 3.30: 12363 3.30 - 3.83: 21449 3.83 - 4.37: 23896 4.37 - 4.90: 40024 Nonbonded interactions: 99939 Sorted by model distance: nonbonded pdb=" O TYR D 229 " pdb=" OG SER D 248 " model vdw 2.237 3.040 nonbonded pdb=" OG1 THR C 383 " pdb=" OE1 GLN C 386 " model vdw 2.249 3.040 nonbonded pdb=" OD1 ASP F 113 " pdb=" OG SER F 116 " model vdw 2.260 3.040 nonbonded pdb=" O LEU E 227 " pdb=" OG1 THR E 231 " model vdw 2.261 3.040 nonbonded pdb=" OG SER B 150 " pdb=" OE1 GLN B 153 " model vdw 2.266 3.040 ... (remaining 99934 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 342 through 354 or resid 362 through 376 or resid 382 thro \ ugh 625)) selection = (chain 'C' and (resid 342 through 354 or resid 362 through 494 or resid 500 thro \ ugh 625)) } ncs_group { reference = (chain 'B' and (resid 59 through 72 or resid 81 through 380 or resid 401)) selection = (chain 'D' and (resid 59 through 72 or resid 81 through 380 or resid 401)) } ncs_group { reference = chain 'E' selection = chain 'F' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.420 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 35.130 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 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 : 0.004 0.060 12657 Z= 0.287 Angle : 0.982 12.420 17062 Z= 0.503 Chirality : 0.055 0.251 1882 Planarity : 0.010 0.318 2171 Dihedral : 14.516 89.027 4817 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.29 % Favored : 95.58 % Rotamer: Outliers : 0.44 % Allowed : 0.44 % Favored : 99.11 % 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: -0.95 (0.20), residues: 1515 helix: -0.11 (0.17), residues: 847 sheet: -0.48 (0.60), residues: 78 loop : -1.30 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.093 0.003 TRP E 230 HIS 0.014 0.001 HIS E 180 PHE 0.039 0.002 PHE F 176 TYR 0.051 0.002 TYR F 48 ARG 0.012 0.001 ARG E 224 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 231 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 GLU cc_start: 0.9082 (tt0) cc_final: 0.8771 (tt0) REVERT: A 447 ASP cc_start: 0.9258 (m-30) cc_final: 0.8903 (m-30) REVERT: A 469 MET cc_start: 0.8571 (ppp) cc_final: 0.8325 (ppp) REVERT: A 486 ASP cc_start: 0.8437 (t0) cc_final: 0.7818 (t0) REVERT: A 512 MET cc_start: 0.7463 (ptp) cc_final: 0.7079 (ptp) REVERT: A 534 TYR cc_start: 0.9160 (t80) cc_final: 0.8235 (t80) REVERT: A 581 MET cc_start: 0.6617 (ptt) cc_final: 0.6305 (ptt) REVERT: B 143 MET cc_start: 0.9009 (tpt) cc_final: 0.8688 (tpp) REVERT: B 341 CYS cc_start: 0.8706 (m) cc_final: 0.8345 (m) REVERT: C 350 MET cc_start: 0.5904 (ppp) cc_final: 0.5400 (ppp) REVERT: C 392 ASN cc_start: 0.9038 (m110) cc_final: 0.8655 (t0) REVERT: C 412 MET cc_start: 0.6581 (ppp) cc_final: 0.6061 (ppp) REVERT: C 442 MET cc_start: 0.8299 (tpt) cc_final: 0.7796 (tmm) REVERT: C 446 ILE cc_start: 0.9506 (mt) cc_final: 0.8367 (mt) REVERT: C 447 ASP cc_start: 0.9039 (t0) cc_final: 0.8535 (t0) REVERT: C 462 LYS cc_start: 0.8945 (tttt) cc_final: 0.8687 (tttt) REVERT: C 464 ILE cc_start: 0.9108 (mm) cc_final: 0.8609 (mp) REVERT: C 532 TYR cc_start: 0.8799 (t80) cc_final: 0.8507 (t80) REVERT: C 552 ASN cc_start: 0.8958 (p0) cc_final: 0.8219 (p0) REVERT: D 65 ASP cc_start: 0.8666 (p0) cc_final: 0.7865 (m-30) REVERT: D 94 MET cc_start: 0.3473 (tpt) cc_final: 0.1539 (mmm) REVERT: D 143 MET cc_start: 0.7849 (tpp) cc_final: 0.7485 (mmt) REVERT: D 208 ASP cc_start: 0.8991 (m-30) cc_final: 0.8756 (m-30) REVERT: D 230 MET cc_start: 0.6926 (tmm) cc_final: 0.4199 (ppp) REVERT: D 247 TRP cc_start: 0.8680 (t60) cc_final: 0.8148 (t60) REVERT: D 249 MET cc_start: 0.9378 (tmm) cc_final: 0.9005 (tmm) REVERT: E 25 PHE cc_start: 0.8383 (m-80) cc_final: 0.8122 (m-80) REVERT: F 124 LYS cc_start: 0.8799 (pptt) cc_final: 0.8234 (pptt) REVERT: F 155 MET cc_start: 0.7434 (ptp) cc_final: 0.6946 (ptp) outliers start: 6 outliers final: 0 residues processed: 233 average time/residue: 0.2285 time to fit residues: 77.6651 Evaluate side-chains 170 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12657 Z= 0.260 Angle : 0.631 7.298 17062 Z= 0.336 Chirality : 0.043 0.139 1882 Planarity : 0.006 0.152 2171 Dihedral : 5.565 63.509 1734 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.29 % Favored : 95.58 % Rotamer: Outliers : 0.07 % Allowed : 4.30 % Favored : 95.63 % 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: 0.04 (0.21), residues: 1515 helix: 0.79 (0.18), residues: 861 sheet: -0.35 (0.59), residues: 76 loop : -1.00 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 230 HIS 0.005 0.001 HIS D 145 PHE 0.018 0.002 PHE F 176 TYR 0.024 0.002 TYR F 48 ARG 0.010 0.001 ARG E 224 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 206 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 GLU cc_start: 0.9131 (tt0) cc_final: 0.8682 (tt0) REVERT: A 447 ASP cc_start: 0.9368 (m-30) cc_final: 0.9038 (m-30) REVERT: A 469 MET cc_start: 0.8853 (ppp) cc_final: 0.8194 (ppp) REVERT: A 486 ASP cc_start: 0.8520 (t0) cc_final: 0.7908 (t0) REVERT: A 534 TYR cc_start: 0.9272 (t80) cc_final: 0.8626 (t80) REVERT: B 341 CYS cc_start: 0.8727 (m) cc_final: 0.8436 (m) REVERT: C 350 MET cc_start: 0.4974 (ppp) cc_final: 0.4588 (ppp) REVERT: C 412 MET cc_start: 0.6389 (ppp) cc_final: 0.5800 (ppp) REVERT: C 442 MET cc_start: 0.8034 (tpt) cc_final: 0.7761 (tmm) REVERT: C 446 ILE cc_start: 0.9530 (mt) cc_final: 0.8342 (mt) REVERT: C 447 ASP cc_start: 0.9125 (t0) cc_final: 0.8596 (t0) REVERT: C 552 ASN cc_start: 0.9045 (p0) cc_final: 0.8367 (p0) REVERT: D 143 MET cc_start: 0.8427 (tpp) cc_final: 0.8086 (tpp) REVERT: D 249 MET cc_start: 0.9372 (tmm) cc_final: 0.8985 (tmm) REVERT: D 256 MET cc_start: 0.9345 (pmm) cc_final: 0.9083 (pmm) REVERT: E 181 TYR cc_start: 0.8691 (t80) cc_final: 0.8323 (t80) REVERT: E 220 MET cc_start: 0.7267 (ptp) cc_final: 0.7063 (ptp) REVERT: F 1 MET cc_start: 0.3658 (tpt) cc_final: 0.3311 (tpt) REVERT: F 124 LYS cc_start: 0.8890 (pptt) cc_final: 0.8629 (pptt) outliers start: 1 outliers final: 0 residues processed: 207 average time/residue: 0.2127 time to fit residues: 65.6349 Evaluate side-chains 150 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 149 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 chunk 137 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 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 0.049 12657 Z= 0.188 Angle : 0.589 6.342 17062 Z= 0.309 Chirality : 0.043 0.140 1882 Planarity : 0.004 0.050 2171 Dihedral : 5.331 62.816 1734 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.03 % Favored : 95.84 % Rotamer: Outliers : 0.07 % Allowed : 3.71 % Favored : 96.22 % 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: 0.32 (0.21), residues: 1515 helix: 1.06 (0.18), residues: 861 sheet: -0.27 (0.57), residues: 81 loop : -0.97 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 511 HIS 0.003 0.001 HIS D 145 PHE 0.017 0.001 PHE F 176 TYR 0.022 0.001 TYR F 48 ARG 0.005 0.000 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 213 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 GLU cc_start: 0.9146 (tt0) cc_final: 0.8664 (tt0) REVERT: A 447 ASP cc_start: 0.9357 (m-30) cc_final: 0.9013 (m-30) REVERT: A 469 MET cc_start: 0.8746 (ppp) cc_final: 0.8093 (ppp) REVERT: A 486 ASP cc_start: 0.8489 (t0) cc_final: 0.7835 (t0) REVERT: A 534 TYR cc_start: 0.9327 (t80) cc_final: 0.8622 (t80) REVERT: B 341 CYS cc_start: 0.8810 (m) cc_final: 0.8556 (m) REVERT: C 350 MET cc_start: 0.5073 (ppp) cc_final: 0.4676 (ppp) REVERT: C 412 MET cc_start: 0.6288 (ppp) cc_final: 0.5664 (ppp) REVERT: C 442 MET cc_start: 0.8007 (tpt) cc_final: 0.7748 (tmm) REVERT: C 446 ILE cc_start: 0.9510 (mt) cc_final: 0.8139 (mt) REVERT: C 447 ASP cc_start: 0.9145 (t0) cc_final: 0.8594 (t0) REVERT: C 552 ASN cc_start: 0.9044 (p0) cc_final: 0.8318 (p0) REVERT: D 94 MET cc_start: 0.3258 (tpt) cc_final: 0.1523 (mmm) REVERT: D 125 TYR cc_start: 0.9068 (m-10) cc_final: 0.8864 (m-10) REVERT: D 143 MET cc_start: 0.8508 (tpp) cc_final: 0.7976 (mmt) REVERT: D 146 MET cc_start: 0.7670 (tpt) cc_final: 0.7093 (tpp) REVERT: D 249 MET cc_start: 0.9453 (tmm) cc_final: 0.9053 (tmm) REVERT: E 1 MET cc_start: 0.6030 (tpp) cc_final: 0.5556 (tmm) REVERT: E 162 MET cc_start: 0.2828 (mtt) cc_final: 0.2426 (mtp) REVERT: E 220 MET cc_start: 0.7221 (ptp) cc_final: 0.6826 (ptp) REVERT: F 1 MET cc_start: 0.3803 (tpt) cc_final: 0.3548 (tpp) REVERT: F 124 LYS cc_start: 0.8941 (pptt) cc_final: 0.8516 (pptt) REVERT: F 155 MET cc_start: 0.7722 (ptp) cc_final: 0.7322 (ptp) outliers start: 1 outliers final: 0 residues processed: 214 average time/residue: 0.2184 time to fit residues: 69.1507 Evaluate side-chains 156 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 65 optimal weight: 0.2980 chunk 92 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 131 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12657 Z= 0.163 Angle : 0.586 6.788 17062 Z= 0.303 Chirality : 0.043 0.142 1882 Planarity : 0.004 0.057 2171 Dihedral : 5.151 63.237 1734 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.16 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % 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: 0.43 (0.21), residues: 1515 helix: 1.14 (0.18), residues: 863 sheet: -0.41 (0.56), residues: 81 loop : -0.87 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 247 HIS 0.005 0.001 HIS E 180 PHE 0.023 0.001 PHE F 176 TYR 0.018 0.001 TYR F 48 ARG 0.004 0.000 ARG F 148 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 GLU cc_start: 0.9113 (tt0) cc_final: 0.8579 (tt0) REVERT: A 447 ASP cc_start: 0.9251 (m-30) cc_final: 0.8906 (m-30) REVERT: A 469 MET cc_start: 0.8631 (ppp) cc_final: 0.7955 (ppp) REVERT: A 486 ASP cc_start: 0.8722 (t0) cc_final: 0.7936 (t0) REVERT: A 534 TYR cc_start: 0.9378 (t80) cc_final: 0.8644 (t80) REVERT: B 190 ASP cc_start: 0.8517 (m-30) cc_final: 0.8173 (m-30) REVERT: C 350 MET cc_start: 0.5273 (ppp) cc_final: 0.4776 (ppp) REVERT: C 412 MET cc_start: 0.6194 (ppp) cc_final: 0.5576 (ppp) REVERT: C 442 MET cc_start: 0.7993 (tpt) cc_final: 0.7762 (tmm) REVERT: C 446 ILE cc_start: 0.9525 (mt) cc_final: 0.8211 (mt) REVERT: C 447 ASP cc_start: 0.9150 (t0) cc_final: 0.8599 (t0) REVERT: D 125 TYR cc_start: 0.9087 (m-10) cc_final: 0.8879 (m-10) REVERT: D 146 MET cc_start: 0.7700 (tpt) cc_final: 0.7170 (tpp) REVERT: D 249 MET cc_start: 0.9434 (tmm) cc_final: 0.8989 (tmm) REVERT: E 162 MET cc_start: 0.2299 (mtt) cc_final: 0.1930 (mtp) REVERT: F 15 GLN cc_start: 0.8344 (mt0) cc_final: 0.8027 (mp10) REVERT: F 124 LYS cc_start: 0.8954 (pptt) cc_final: 0.8505 (pptt) REVERT: F 155 MET cc_start: 0.7715 (ptp) cc_final: 0.7401 (ptp) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.2061 time to fit residues: 65.6920 Evaluate side-chains 155 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 131 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12657 Z= 0.194 Angle : 0.604 6.957 17062 Z= 0.313 Chirality : 0.043 0.185 1882 Planarity : 0.004 0.048 2171 Dihedral : 5.128 63.153 1734 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.75 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % 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: 0.53 (0.21), residues: 1515 helix: 1.26 (0.18), residues: 860 sheet: -0.46 (0.55), residues: 81 loop : -0.87 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 230 HIS 0.005 0.001 HIS C 460 PHE 0.018 0.001 PHE F 176 TYR 0.014 0.001 TYR F 127 ARG 0.006 0.000 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 GLU cc_start: 0.9139 (tt0) cc_final: 0.8694 (tt0) REVERT: A 447 ASP cc_start: 0.9331 (m-30) cc_final: 0.9013 (m-30) REVERT: A 469 MET cc_start: 0.8694 (ppp) cc_final: 0.7958 (ppp) REVERT: A 486 ASP cc_start: 0.8730 (t0) cc_final: 0.7946 (t0) REVERT: B 190 ASP cc_start: 0.8629 (m-30) cc_final: 0.8352 (m-30) REVERT: B 204 ILE cc_start: 0.8959 (mp) cc_final: 0.8718 (mp) REVERT: C 350 MET cc_start: 0.5351 (ppp) cc_final: 0.4867 (ppp) REVERT: C 412 MET cc_start: 0.6239 (ppp) cc_final: 0.5817 (ppp) REVERT: C 442 MET cc_start: 0.7982 (tpt) cc_final: 0.7763 (tmm) REVERT: C 446 ILE cc_start: 0.9537 (mt) cc_final: 0.8286 (mt) REVERT: C 447 ASP cc_start: 0.9179 (t0) cc_final: 0.8624 (t0) REVERT: D 125 TYR cc_start: 0.9071 (m-10) cc_final: 0.8859 (m-10) REVERT: D 146 MET cc_start: 0.7800 (tpt) cc_final: 0.7272 (tpp) REVERT: D 249 MET cc_start: 0.9434 (tmm) cc_final: 0.9038 (tmm) REVERT: E 1 MET cc_start: 0.5451 (tpp) cc_final: 0.4852 (tmm) REVERT: E 144 ILE cc_start: 0.8953 (pt) cc_final: 0.8532 (tt) REVERT: F 124 LYS cc_start: 0.8869 (pptt) cc_final: 0.8611 (pptt) REVERT: F 155 MET cc_start: 0.7772 (ptp) cc_final: 0.7278 (ptp) REVERT: F 181 TYR cc_start: 0.8242 (t80) cc_final: 0.7603 (t80) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2090 time to fit residues: 64.5772 Evaluate side-chains 151 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 36 optimal weight: 0.0970 chunk 147 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12657 Z= 0.356 Angle : 0.734 8.046 17062 Z= 0.388 Chirality : 0.047 0.154 1882 Planarity : 0.005 0.047 2171 Dihedral : 5.656 64.092 1734 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.21 % Favored : 94.72 % Rotamer: Outliers : 0.07 % Allowed : 2.37 % Favored : 97.55 % 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: -0.01 (0.21), residues: 1515 helix: 0.80 (0.17), residues: 858 sheet: -0.68 (0.51), residues: 92 loop : -1.07 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 511 HIS 0.007 0.002 HIS A 402 PHE 0.039 0.002 PHE F 176 TYR 0.020 0.002 TYR B 240 ARG 0.009 0.001 ARG E 169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 GLU cc_start: 0.9236 (tt0) cc_final: 0.8714 (tt0) REVERT: A 447 ASP cc_start: 0.9342 (m-30) cc_final: 0.9074 (m-30) REVERT: A 456 MET cc_start: 0.8955 (mmt) cc_final: 0.8655 (mmt) REVERT: A 469 MET cc_start: 0.8737 (ppp) cc_final: 0.8065 (ppp) REVERT: A 486 ASP cc_start: 0.8566 (t0) cc_final: 0.7935 (t0) REVERT: B 341 CYS cc_start: 0.8805 (m) cc_final: 0.8583 (m) REVERT: C 350 MET cc_start: 0.5922 (ppp) cc_final: 0.5336 (ppp) REVERT: C 412 MET cc_start: 0.6350 (ppp) cc_final: 0.5857 (ppp) REVERT: C 442 MET cc_start: 0.8211 (tpt) cc_final: 0.7873 (tmm) REVERT: C 446 ILE cc_start: 0.9535 (mt) cc_final: 0.8398 (mt) REVERT: C 447 ASP cc_start: 0.9273 (t0) cc_final: 0.8768 (t0) REVERT: D 125 TYR cc_start: 0.8994 (m-10) cc_final: 0.8750 (m-10) REVERT: D 146 MET cc_start: 0.8185 (tpt) cc_final: 0.7693 (tpp) REVERT: D 219 MET cc_start: 0.9044 (ptp) cc_final: 0.8600 (ptp) REVERT: D 249 MET cc_start: 0.9480 (tmm) cc_final: 0.9038 (tmm) REVERT: E 1 MET cc_start: 0.5978 (tpp) cc_final: 0.5519 (tmm) REVERT: E 144 ILE cc_start: 0.8938 (pt) cc_final: 0.8425 (tt) REVERT: E 153 GLU cc_start: 0.9387 (mp0) cc_final: 0.9153 (mp0) REVERT: E 180 HIS cc_start: 0.7510 (m170) cc_final: 0.7082 (m170) outliers start: 1 outliers final: 0 residues processed: 194 average time/residue: 0.2176 time to fit residues: 62.9315 Evaluate side-chains 142 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 6.9990 chunk 16 optimal weight: 0.3980 chunk 83 optimal weight: 0.6980 chunk 107 optimal weight: 8.9990 chunk 123 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 146 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12657 Z= 0.186 Angle : 0.630 8.960 17062 Z= 0.326 Chirality : 0.044 0.162 1882 Planarity : 0.004 0.045 2171 Dihedral : 5.300 64.197 1734 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.49 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % 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: 0.26 (0.21), residues: 1515 helix: 1.07 (0.18), residues: 856 sheet: -0.81 (0.51), residues: 92 loop : -1.00 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 511 HIS 0.007 0.001 HIS D 119 PHE 0.016 0.002 PHE A 599 TYR 0.017 0.001 TYR E 84 ARG 0.008 0.000 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 GLU cc_start: 0.9182 (tt0) cc_final: 0.8887 (tt0) REVERT: A 447 ASP cc_start: 0.9319 (m-30) cc_final: 0.9036 (m-30) REVERT: A 456 MET cc_start: 0.8897 (mmt) cc_final: 0.8533 (mmt) REVERT: A 469 MET cc_start: 0.8624 (ppp) cc_final: 0.7963 (ppp) REVERT: A 486 ASP cc_start: 0.8442 (t0) cc_final: 0.7809 (t0) REVERT: A 574 TYR cc_start: 0.7344 (p90) cc_final: 0.6784 (p90) REVERT: B 204 ILE cc_start: 0.8997 (mp) cc_final: 0.8748 (mp) REVERT: C 350 MET cc_start: 0.6247 (ppp) cc_final: 0.5709 (ppp) REVERT: C 412 MET cc_start: 0.6123 (ppp) cc_final: 0.5442 (ppp) REVERT: C 442 MET cc_start: 0.8075 (tpt) cc_final: 0.7822 (tmm) REVERT: C 446 ILE cc_start: 0.9539 (mt) cc_final: 0.8292 (mt) REVERT: C 447 ASP cc_start: 0.9248 (t0) cc_final: 0.8738 (t0) REVERT: C 462 LYS cc_start: 0.9138 (tttt) cc_final: 0.8872 (ttmt) REVERT: C 464 ILE cc_start: 0.9096 (mm) cc_final: 0.8686 (mp) REVERT: D 125 TYR cc_start: 0.8966 (m-10) cc_final: 0.8675 (m-10) REVERT: D 146 MET cc_start: 0.7898 (tpt) cc_final: 0.7361 (tpp) REVERT: D 219 MET cc_start: 0.9113 (ptp) cc_final: 0.8837 (ptp) REVERT: D 249 MET cc_start: 0.9449 (tmm) cc_final: 0.9006 (tmm) REVERT: E 1 MET cc_start: 0.5947 (tpp) cc_final: 0.5515 (tmm) REVERT: E 144 ILE cc_start: 0.8976 (pt) cc_final: 0.8604 (tt) REVERT: E 180 HIS cc_start: 0.7657 (m170) cc_final: 0.7371 (m170) REVERT: F 153 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8176 (mt-10) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.2186 time to fit residues: 68.5038 Evaluate side-chains 153 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 140 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12657 Z= 0.191 Angle : 0.654 10.291 17062 Z= 0.338 Chirality : 0.044 0.146 1882 Planarity : 0.004 0.043 2171 Dihedral : 5.226 65.343 1734 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.02 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % 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: 0.30 (0.21), residues: 1515 helix: 1.08 (0.18), residues: 858 sheet: -0.70 (0.51), residues: 90 loop : -0.96 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 511 HIS 0.003 0.001 HIS D 145 PHE 0.032 0.002 PHE F 176 TYR 0.024 0.001 TYR B 240 ARG 0.006 0.000 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 GLU cc_start: 0.9157 (tt0) cc_final: 0.8673 (tt0) REVERT: A 447 ASP cc_start: 0.9291 (m-30) cc_final: 0.8949 (m-30) REVERT: A 456 MET cc_start: 0.8913 (mmt) cc_final: 0.8670 (mmt) REVERT: A 469 MET cc_start: 0.8648 (ppp) cc_final: 0.8001 (ppp) REVERT: A 486 ASP cc_start: 0.8434 (t0) cc_final: 0.7817 (t0) REVERT: A 574 TYR cc_start: 0.7168 (p90) cc_final: 0.6383 (p90) REVERT: B 110 GLN cc_start: 0.8703 (tp-100) cc_final: 0.8489 (tp-100) REVERT: C 350 MET cc_start: 0.6254 (ppp) cc_final: 0.5735 (ppp) REVERT: C 412 MET cc_start: 0.6074 (ppp) cc_final: 0.5428 (ppp) REVERT: C 442 MET cc_start: 0.8022 (tpt) cc_final: 0.7621 (tmm) REVERT: C 446 ILE cc_start: 0.9536 (mt) cc_final: 0.8244 (mt) REVERT: C 447 ASP cc_start: 0.9248 (t0) cc_final: 0.8745 (t0) REVERT: D 125 TYR cc_start: 0.8970 (m-10) cc_final: 0.8667 (m-10) REVERT: D 146 MET cc_start: 0.7918 (tpt) cc_final: 0.7369 (tpp) REVERT: D 219 MET cc_start: 0.9127 (ptp) cc_final: 0.8752 (ptp) REVERT: D 228 SER cc_start: 0.9221 (p) cc_final: 0.8911 (m) REVERT: D 249 MET cc_start: 0.9459 (tmm) cc_final: 0.8989 (tmm) REVERT: E 144 ILE cc_start: 0.8955 (pt) cc_final: 0.8585 (tt) REVERT: E 180 HIS cc_start: 0.7633 (m170) cc_final: 0.7312 (m170) REVERT: F 1 MET cc_start: 0.4862 (tpp) cc_final: 0.4177 (tmm) REVERT: F 155 MET cc_start: 0.7673 (ptp) cc_final: 0.7323 (ptp) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.2161 time to fit residues: 66.4257 Evaluate side-chains 149 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.0070 chunk 136 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 123 optimal weight: 0.1980 chunk 129 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 144 optimal weight: 7.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12657 Z= 0.173 Angle : 0.660 11.122 17062 Z= 0.337 Chirality : 0.044 0.156 1882 Planarity : 0.004 0.081 2171 Dihedral : 5.169 66.979 1734 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.42 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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: 0.33 (0.21), residues: 1515 helix: 1.10 (0.18), residues: 858 sheet: -0.74 (0.55), residues: 80 loop : -0.93 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 511 HIS 0.005 0.001 HIS C 460 PHE 0.030 0.002 PHE F 176 TYR 0.018 0.001 TYR A 574 ARG 0.006 0.000 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 GLU cc_start: 0.9141 (tt0) cc_final: 0.8634 (tt0) REVERT: A 447 ASP cc_start: 0.9187 (m-30) cc_final: 0.8837 (m-30) REVERT: A 469 MET cc_start: 0.8537 (ppp) cc_final: 0.7946 (ppp) REVERT: A 486 ASP cc_start: 0.8419 (t0) cc_final: 0.7798 (t0) REVERT: A 532 TYR cc_start: 0.8536 (t80) cc_final: 0.8236 (t80) REVERT: B 110 GLN cc_start: 0.8833 (tp-100) cc_final: 0.8492 (tp-100) REVERT: B 190 ASP cc_start: 0.8166 (m-30) cc_final: 0.7906 (m-30) REVERT: C 350 MET cc_start: 0.6426 (ppp) cc_final: 0.5809 (ppp) REVERT: C 412 MET cc_start: 0.5951 (ppp) cc_final: 0.5325 (ppp) REVERT: C 442 MET cc_start: 0.7926 (tpt) cc_final: 0.7489 (tmm) REVERT: C 446 ILE cc_start: 0.9534 (mt) cc_final: 0.8176 (mt) REVERT: C 447 ASP cc_start: 0.9233 (t0) cc_final: 0.8740 (t0) REVERT: D 125 TYR cc_start: 0.8958 (m-10) cc_final: 0.8641 (m-10) REVERT: D 146 MET cc_start: 0.7901 (tpt) cc_final: 0.7348 (tpp) REVERT: D 219 MET cc_start: 0.9117 (ptp) cc_final: 0.8758 (ptp) REVERT: D 228 SER cc_start: 0.9274 (p) cc_final: 0.9031 (m) REVERT: D 249 MET cc_start: 0.9427 (tmm) cc_final: 0.9027 (tmm) REVERT: E 144 ILE cc_start: 0.8936 (pt) cc_final: 0.8479 (tt) REVERT: E 180 HIS cc_start: 0.7680 (m170) cc_final: 0.7458 (m170) REVERT: F 26 MET cc_start: 0.9085 (mtp) cc_final: 0.8852 (mtp) REVERT: F 119 PHE cc_start: 0.8782 (t80) cc_final: 0.8495 (t80) REVERT: F 155 MET cc_start: 0.7721 (ptp) cc_final: 0.7393 (ptp) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.2033 time to fit residues: 65.4524 Evaluate side-chains 152 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 93 optimal weight: 0.0980 chunk 73 optimal weight: 0.2980 chunk 95 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12657 Z= 0.167 Angle : 0.663 10.634 17062 Z= 0.335 Chirality : 0.044 0.158 1882 Planarity : 0.004 0.077 2171 Dihedral : 5.079 68.684 1734 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.42 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 (0.22), residues: 1515 helix: 1.18 (0.18), residues: 858 sheet: -0.68 (0.55), residues: 80 loop : -0.89 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 511 HIS 0.005 0.001 HIS E 180 PHE 0.025 0.002 PHE F 176 TYR 0.021 0.001 TYR A 534 ARG 0.005 0.000 ARG E 148 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 GLU cc_start: 0.9100 (tt0) cc_final: 0.8583 (tt0) REVERT: A 447 ASP cc_start: 0.9176 (m-30) cc_final: 0.8833 (m-30) REVERT: A 468 ASP cc_start: 0.8517 (p0) cc_final: 0.8191 (p0) REVERT: A 469 MET cc_start: 0.8691 (ppp) cc_final: 0.8064 (ppp) REVERT: A 486 ASP cc_start: 0.8405 (t0) cc_final: 0.7758 (t0) REVERT: A 532 TYR cc_start: 0.8546 (t80) cc_final: 0.8230 (t80) REVERT: A 581 MET cc_start: 0.6697 (ptt) cc_final: 0.6433 (ptt) REVERT: B 110 GLN cc_start: 0.8843 (tp-100) cc_final: 0.8499 (tp-100) REVERT: B 190 ASP cc_start: 0.8188 (m-30) cc_final: 0.7930 (m-30) REVERT: B 308 MET cc_start: 0.7058 (tmm) cc_final: 0.5488 (mmp) REVERT: C 350 MET cc_start: 0.6392 (ppp) cc_final: 0.5800 (ppp) REVERT: C 412 MET cc_start: 0.5922 (ppp) cc_final: 0.5345 (ppp) REVERT: C 442 MET cc_start: 0.7991 (tpt) cc_final: 0.7551 (tmm) REVERT: C 446 ILE cc_start: 0.9543 (mt) cc_final: 0.8183 (mt) REVERT: C 447 ASP cc_start: 0.9225 (t0) cc_final: 0.8733 (t0) REVERT: D 103 ILE cc_start: 0.6841 (tp) cc_final: 0.6402 (pt) REVERT: D 125 TYR cc_start: 0.8951 (m-10) cc_final: 0.8628 (m-10) REVERT: D 146 MET cc_start: 0.7910 (tpt) cc_final: 0.7348 (tpp) REVERT: D 219 MET cc_start: 0.9105 (ptp) cc_final: 0.8730 (ptp) REVERT: D 228 SER cc_start: 0.9237 (p) cc_final: 0.9008 (m) REVERT: D 249 MET cc_start: 0.9452 (tmm) cc_final: 0.9047 (tmm) REVERT: E 144 ILE cc_start: 0.8928 (pt) cc_final: 0.8472 (tt) REVERT: E 180 HIS cc_start: 0.7687 (m170) cc_final: 0.7314 (m170) REVERT: F 1 MET cc_start: 0.5528 (tpp) cc_final: 0.4966 (tmm) REVERT: F 26 MET cc_start: 0.9087 (mtp) cc_final: 0.8842 (mtp) REVERT: F 155 MET cc_start: 0.7778 (ptp) cc_final: 0.7284 (ptp) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.2092 time to fit residues: 65.5607 Evaluate side-chains 151 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 6 optimal weight: 0.0050 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.074130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.054340 restraints weight = 64313.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.056016 restraints weight = 40442.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.057191 restraints weight = 29277.806| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12657 Z= 0.204 Angle : 0.673 10.591 17062 Z= 0.343 Chirality : 0.044 0.160 1882 Planarity : 0.004 0.071 2171 Dihedral : 5.141 69.595 1734 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.08 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % 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: 0.37 (0.21), residues: 1515 helix: 1.14 (0.18), residues: 857 sheet: -0.82 (0.51), residues: 90 loop : -0.90 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 511 HIS 0.003 0.001 HIS E 180 PHE 0.021 0.002 PHE F 176 TYR 0.019 0.002 TYR F 120 ARG 0.004 0.000 ARG E 148 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2266.19 seconds wall clock time: 41 minutes 10.92 seconds (2470.92 seconds total)