Starting phenix.real_space_refine on Thu Mar 14 21:48:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cv2_27006/03_2024/8cv2_27006.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cv2_27006/03_2024/8cv2_27006.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cv2_27006/03_2024/8cv2_27006.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cv2_27006/03_2024/8cv2_27006.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cv2_27006/03_2024/8cv2_27006.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cv2_27006/03_2024/8cv2_27006.pdb" } resolution = 2.44 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= 0.010 sd= 0.111 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 S 63 5.16 5 Na 6 4.78 5 C 6459 2.51 5 N 1578 2.21 5 O 1776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 40": "OE1" <-> "OE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A GLU 274": "OE1" <-> "OE2" Residue "B GLU 40": "OE1" <-> "OE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B GLU 274": "OE1" <-> "OE2" Residue "C GLU 40": "OE1" <-> "OE2" Residue "C GLU 167": "OE1" <-> "OE2" Residue "C GLU 274": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9882 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3292 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 12, 'TRANS': 420} Chain breaks: 1 Chain: "B" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3292 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 12, 'TRANS': 420} Chain breaks: 1 Chain: "C" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3292 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 12, 'TRANS': 420} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.17, per 1000 atoms: 0.52 Number of scatterers: 9882 At special positions: 0 Unit cell: (109.056, 105.648, 80.94, 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 63 16.00 Na 6 11.00 O 1776 8.00 N 1578 7.00 C 6459 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: 4.28 Conformation dependent library (CDL) restraints added in 1.7 seconds 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 3 sheets defined 84.3% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 18 through 42 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.739A pdb=" N ALA A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 65 Processing helix chain 'A' and resid 66 through 82 removed outlier: 3.839A pdb=" N LEU A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 117 Processing helix chain 'A' and resid 137 through 150 removed outlier: 3.542A pdb=" N PHE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 removed outlier: 3.608A pdb=" N ALA A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 229 removed outlier: 3.597A pdb=" N LYS A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 273 removed outlier: 4.029A pdb=" N TRP A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 3.547A pdb=" N PHE A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL A 273 " --> pdb=" O CYS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 282 Processing helix chain 'A' and resid 282 through 309 removed outlier: 4.898A pdb=" N LEU A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Proline residue: A 302 - end of helix Processing helix chain 'A' and resid 312 through 320 removed outlier: 4.053A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 351 through 366 removed outlier: 3.703A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Proline residue: A 360 - end of helix Processing helix chain 'A' and resid 367 through 385 Processing helix chain 'A' and resid 390 through 408 Processing helix chain 'A' and resid 413 through 427 Processing helix chain 'A' and resid 429 through 438 removed outlier: 3.542A pdb=" N THR A 434 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A 437 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ALA A 438 " --> pdb=" O LEU A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 466 removed outlier: 4.596A pdb=" N ARG A 445 " --> pdb=" O CYS A 441 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 476 removed outlier: 3.803A pdb=" N LEU A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 42 Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.738A pdb=" N ALA B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 65 Processing helix chain 'B' and resid 66 through 82 removed outlier: 3.838A pdb=" N LEU B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 117 Processing helix chain 'B' and resid 137 through 150 removed outlier: 3.543A pdb=" N PHE B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 158 removed outlier: 3.608A pdb=" N ALA B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 229 removed outlier: 3.597A pdb=" N LYS B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 273 removed outlier: 4.028A pdb=" N TRP B 256 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N TYR B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) Proline residue: B 259 - end of helix removed outlier: 3.546A pdb=" N PHE B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL B 273 " --> pdb=" O CYS B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 282 Processing helix chain 'B' and resid 282 through 309 removed outlier: 4.897A pdb=" N LEU B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Proline residue: B 302 - end of helix Processing helix chain 'B' and resid 312 through 320 removed outlier: 4.052A pdb=" N PHE B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 331 Processing helix chain 'B' and resid 336 through 347 Processing helix chain 'B' and resid 351 through 366 removed outlier: 3.703A pdb=" N PHE B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Proline residue: B 360 - end of helix Processing helix chain 'B' and resid 367 through 385 Processing helix chain 'B' and resid 390 through 408 Processing helix chain 'B' and resid 413 through 427 Processing helix chain 'B' and resid 429 through 438 removed outlier: 3.542A pdb=" N THR B 434 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE B 437 " --> pdb=" O THR B 434 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ALA B 438 " --> pdb=" O LEU B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 466 removed outlier: 4.596A pdb=" N ARG B 445 " --> pdb=" O CYS B 441 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 476 removed outlier: 3.802A pdb=" N LEU B 470 " --> pdb=" O SER B 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 42 Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.738A pdb=" N ALA C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 65 Processing helix chain 'C' and resid 66 through 82 removed outlier: 3.839A pdb=" N LEU C 82 " --> pdb=" O GLY C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 117 Processing helix chain 'C' and resid 137 through 150 removed outlier: 3.543A pdb=" N PHE C 150 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 158 removed outlier: 3.608A pdb=" N ALA C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 229 removed outlier: 3.596A pdb=" N LYS C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 273 removed outlier: 4.028A pdb=" N TRP C 256 " --> pdb=" O GLN C 252 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N TYR C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) Proline residue: C 259 - end of helix removed outlier: 3.546A pdb=" N PHE C 264 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL C 273 " --> pdb=" O CYS C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 282 Processing helix chain 'C' and resid 282 through 309 removed outlier: 4.897A pdb=" N LEU C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Proline residue: C 302 - end of helix Processing helix chain 'C' and resid 312 through 320 removed outlier: 4.052A pdb=" N PHE C 316 " --> pdb=" O ASN C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 331 Processing helix chain 'C' and resid 336 through 347 Processing helix chain 'C' and resid 351 through 366 removed outlier: 3.703A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Proline residue: C 360 - end of helix Processing helix chain 'C' and resid 367 through 385 Processing helix chain 'C' and resid 390 through 408 Processing helix chain 'C' and resid 413 through 427 Processing helix chain 'C' and resid 429 through 438 removed outlier: 3.541A pdb=" N THR C 434 " --> pdb=" O GLU C 431 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE C 437 " --> pdb=" O THR C 434 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ALA C 438 " --> pdb=" O LEU C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 466 removed outlier: 4.596A pdb=" N ARG C 445 " --> pdb=" O CYS C 441 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 476 removed outlier: 3.802A pdb=" N LEU C 470 " --> pdb=" O SER C 466 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 Processing sheet with id=AA2, first strand: chain 'B' and resid 160 through 167 Processing sheet with id=AA3, first strand: chain 'C' and resid 160 through 167 783 hydrogen bonds defined for protein. 2304 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: 2.38 Time building geometry restraints manager: 4.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3092 1.34 - 1.46: 1443 1.46 - 1.58: 5371 1.58 - 1.69: 0 1.69 - 1.81: 117 Bond restraints: 10023 Sorted by residual: bond pdb=" N GLU C 274 " pdb=" CA GLU C 274 " ideal model delta sigma weight residual 1.458 1.490 -0.031 1.26e-02 6.30e+03 6.20e+00 bond pdb=" N GLU B 274 " pdb=" CA GLU B 274 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.26e-02 6.30e+03 5.97e+00 bond pdb=" N GLU A 274 " pdb=" CA GLU A 274 " ideal model delta sigma weight residual 1.458 1.489 -0.030 1.26e-02 6.30e+03 5.79e+00 bond pdb=" N SER C 331 " pdb=" CA SER C 331 " ideal model delta sigma weight residual 1.460 1.489 -0.030 1.48e-02 4.57e+03 4.10e+00 bond pdb=" N SER A 331 " pdb=" CA SER A 331 " ideal model delta sigma weight residual 1.460 1.489 -0.030 1.48e-02 4.57e+03 4.09e+00 ... (remaining 10018 not shown) Histogram of bond angle deviations from ideal: 100.21 - 106.96: 219 106.96 - 113.71: 5908 113.71 - 120.46: 3852 120.46 - 127.22: 3572 127.22 - 133.97: 57 Bond angle restraints: 13608 Sorted by residual: angle pdb=" CB GLU C 471 " pdb=" CG GLU C 471 " pdb=" CD GLU C 471 " ideal model delta sigma weight residual 112.60 116.51 -3.91 1.70e+00 3.46e-01 5.29e+00 angle pdb=" CB GLU B 471 " pdb=" CG GLU B 471 " pdb=" CD GLU B 471 " ideal model delta sigma weight residual 112.60 116.51 -3.91 1.70e+00 3.46e-01 5.29e+00 angle pdb=" CB GLU A 471 " pdb=" CG GLU A 471 " pdb=" CD GLU A 471 " ideal model delta sigma weight residual 112.60 116.51 -3.91 1.70e+00 3.46e-01 5.28e+00 angle pdb=" CA GLU C 274 " pdb=" C GLU C 274 " pdb=" O GLU C 274 " ideal model delta sigma weight residual 120.24 117.74 2.50 1.11e+00 8.12e-01 5.06e+00 angle pdb=" CA SER A 331 " pdb=" C SER A 331 " pdb=" O SER A 331 " ideal model delta sigma weight residual 120.57 117.90 2.67 1.20e+00 6.94e-01 4.96e+00 ... (remaining 13603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.74: 5287 15.74 - 31.48: 512 31.48 - 47.22: 177 47.22 - 62.96: 21 62.96 - 78.70: 6 Dihedral angle restraints: 6003 sinusoidal: 2280 harmonic: 3723 Sorted by residual: dihedral pdb=" CA VAL C 299 " pdb=" C VAL C 299 " pdb=" N ILE C 300 " pdb=" CA ILE C 300 " ideal model delta harmonic sigma weight residual -180.00 -162.82 -17.18 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA VAL A 299 " pdb=" C VAL A 299 " pdb=" N ILE A 300 " pdb=" CA ILE A 300 " ideal model delta harmonic sigma weight residual -180.00 -162.85 -17.15 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA VAL B 299 " pdb=" C VAL B 299 " pdb=" N ILE B 300 " pdb=" CA ILE B 300 " ideal model delta harmonic sigma weight residual -180.00 -162.86 -17.14 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 6000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1130 0.029 - 0.058: 378 0.058 - 0.087: 156 0.087 - 0.116: 46 0.116 - 0.145: 15 Chirality restraints: 1725 Sorted by residual: chirality pdb=" CA VAL B 411 " pdb=" N VAL B 411 " pdb=" C VAL B 411 " pdb=" CB VAL B 411 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA VAL A 411 " pdb=" N VAL A 411 " pdb=" C VAL A 411 " pdb=" CB VAL A 411 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA VAL C 411 " pdb=" N VAL C 411 " pdb=" C VAL C 411 " pdb=" CB VAL C 411 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 1722 not shown) Planarity restraints: 1665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 401 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C ALA C 401 " -0.033 2.00e-02 2.50e+03 pdb=" O ALA C 401 " 0.012 2.00e-02 2.50e+03 pdb=" N THR C 402 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 296 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.48e+00 pdb=" C HIS C 296 " 0.032 2.00e-02 2.50e+03 pdb=" O HIS C 296 " -0.012 2.00e-02 2.50e+03 pdb=" N SER C 297 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 401 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.46e+00 pdb=" C ALA A 401 " -0.032 2.00e-02 2.50e+03 pdb=" O ALA A 401 " 0.012 2.00e-02 2.50e+03 pdb=" N THR A 402 " 0.011 2.00e-02 2.50e+03 ... (remaining 1662 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2453 2.80 - 3.33: 9997 3.33 - 3.85: 16120 3.85 - 4.38: 18160 4.38 - 4.90: 32528 Nonbonded interactions: 79258 Sorted by model distance: nonbonded pdb=" NH2 ARG C 39 " pdb=" O VAL C 273 " model vdw 2.281 2.520 nonbonded pdb=" NH2 ARG A 39 " pdb=" O VAL A 273 " model vdw 2.281 2.520 nonbonded pdb=" NH2 ARG B 39 " pdb=" O VAL B 273 " model vdw 2.282 2.520 nonbonded pdb=" OD1 ASP C 368 " pdb="NA NA C 602 " model vdw 2.321 2.470 nonbonded pdb=" OD1 ASP A 368 " pdb="NA NA A 602 " model vdw 2.322 2.470 ... (remaining 79253 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' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 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: 6.000 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 27.560 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: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 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 : 0.003 0.045 10023 Z= 0.196 Angle : 0.533 5.744 13608 Z= 0.297 Chirality : 0.037 0.145 1725 Planarity : 0.004 0.033 1665 Dihedral : 14.128 78.698 3603 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.00 % Allowed : 19.11 % Favored : 80.89 % 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: 1.88 (0.23), residues: 1287 helix: 1.83 (0.16), residues: 1029 sheet: 1.73 (0.53), residues: 48 loop : -1.87 (0.31), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 19 HIS 0.002 0.001 HIS C 41 PHE 0.011 0.001 PHE C 341 TYR 0.009 0.001 TYR B 373 ARG 0.005 0.001 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.077 Fit side-chains REVERT: A 274 GLU cc_start: 0.7289 (pm20) cc_final: 0.6901 (pm20) REVERT: B 205 MET cc_start: 0.8442 (ptm) cc_final: 0.8216 (ptm) REVERT: B 258 MET cc_start: 0.8659 (ttm) cc_final: 0.8437 (ttp) REVERT: B 274 GLU cc_start: 0.7284 (pm20) cc_final: 0.6752 (pm20) REVERT: B 473 MET cc_start: 0.7174 (ttp) cc_final: 0.6904 (ttm) REVERT: C 274 GLU cc_start: 0.7233 (pm20) cc_final: 0.6833 (pm20) REVERT: C 449 MET cc_start: 0.8214 (ttp) cc_final: 0.7898 (tmt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 1.2223 time to fit residues: 174.2839 Evaluate side-chains 125 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 54 optimal weight: 0.0870 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 75 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 312 ASN C 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10023 Z= 0.225 Angle : 0.526 5.565 13608 Z= 0.284 Chirality : 0.038 0.131 1725 Planarity : 0.004 0.032 1665 Dihedral : 3.811 18.015 1365 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 3.05 % Allowed : 15.70 % Favored : 81.26 % 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: 2.59 (0.23), residues: 1287 helix: 2.27 (0.16), residues: 1011 sheet: 1.63 (0.52), residues: 48 loop : -0.91 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 19 HIS 0.002 0.001 HIS B 296 PHE 0.013 0.002 PHE C 240 TYR 0.009 0.001 TYR A 373 ARG 0.005 0.001 ARG C 315 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 123 time to evaluate : 1.057 Fit side-chains REVERT: A 330 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7717 (mt) REVERT: B 330 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7695 (mt) REVERT: B 442 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7686 (tp) REVERT: C 274 GLU cc_start: 0.7311 (pm20) cc_final: 0.7015 (pm20) REVERT: C 449 MET cc_start: 0.8164 (ttp) cc_final: 0.7815 (tmt) outliers start: 33 outliers final: 13 residues processed: 145 average time/residue: 1.1320 time to fit residues: 176.7300 Evaluate side-chains 135 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 441 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 126 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 312 ASN C 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10023 Z= 0.310 Angle : 0.591 6.876 13608 Z= 0.319 Chirality : 0.041 0.158 1725 Planarity : 0.004 0.035 1665 Dihedral : 4.032 18.599 1365 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 4.16 % Allowed : 16.53 % Favored : 79.32 % 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: 2.27 (0.23), residues: 1287 helix: 2.03 (0.16), residues: 1017 sheet: 1.26 (0.52), residues: 48 loop : -0.94 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 19 HIS 0.003 0.001 HIS C 296 PHE 0.014 0.002 PHE A 240 TYR 0.010 0.002 TYR C 305 ARG 0.004 0.001 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 129 time to evaluate : 0.992 Fit side-chains REVERT: A 330 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7757 (mt) REVERT: B 330 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7750 (mt) REVERT: B 442 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7872 (tp) outliers start: 45 outliers final: 23 residues processed: 158 average time/residue: 1.0789 time to fit residues: 184.5086 Evaluate side-chains 154 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 128 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 467 LYS Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 441 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 111 optimal weight: 0.3980 chunk 33 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN A 322 GLN B 312 ASN C 312 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10023 Z= 0.169 Angle : 0.481 5.614 13608 Z= 0.260 Chirality : 0.037 0.155 1725 Planarity : 0.004 0.032 1665 Dihedral : 3.799 18.338 1365 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.22 % Allowed : 18.74 % Favored : 79.04 % 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: 2.70 (0.23), residues: 1287 helix: 2.40 (0.16), residues: 1011 sheet: 1.36 (0.55), residues: 48 loop : -1.05 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 256 HIS 0.001 0.001 HIS C 296 PHE 0.009 0.001 PHE A 218 TYR 0.007 0.001 TYR A 373 ARG 0.005 0.000 ARG B 315 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 1.161 Fit side-chains REVERT: A 258 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8386 (ttm) REVERT: A 330 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7724 (mt) REVERT: B 442 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7670 (tp) REVERT: C 274 GLU cc_start: 0.7161 (pm20) cc_final: 0.6908 (pm20) REVERT: C 329 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7755 (mmm) REVERT: C 432 ASP cc_start: 0.7518 (m-30) cc_final: 0.7017 (m-30) outliers start: 24 outliers final: 9 residues processed: 145 average time/residue: 1.1847 time to fit residues: 184.5502 Evaluate side-chains 142 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 329 MET Chi-restraints excluded: chain C residue 441 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 63 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN A 322 GLN B 312 ASN C 312 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10023 Z= 0.167 Angle : 0.475 5.345 13608 Z= 0.256 Chirality : 0.037 0.143 1725 Planarity : 0.003 0.030 1665 Dihedral : 3.701 17.437 1365 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.59 % Allowed : 19.02 % Favored : 78.39 % 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: 2.79 (0.23), residues: 1287 helix: 2.49 (0.16), residues: 1011 sheet: 1.39 (0.55), residues: 48 loop : -1.17 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 256 HIS 0.001 0.000 HIS B 296 PHE 0.010 0.001 PHE C 240 TYR 0.009 0.001 TYR A 373 ARG 0.006 0.000 ARG C 315 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 131 time to evaluate : 1.156 Fit side-chains REVERT: A 330 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7675 (mt) REVERT: B 330 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7705 (mt) REVERT: B 442 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7607 (tp) REVERT: C 449 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7520 (tmm) outliers start: 28 outliers final: 14 residues processed: 145 average time/residue: 1.1514 time to fit residues: 179.8458 Evaluate side-chains 147 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 129 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 441 CYS Chi-restraints excluded: chain C residue 449 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 312 ASN C 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10023 Z= 0.195 Angle : 0.497 5.453 13608 Z= 0.268 Chirality : 0.037 0.141 1725 Planarity : 0.004 0.029 1665 Dihedral : 3.752 17.555 1365 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.59 % Allowed : 19.39 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.23), residues: 1287 helix: 2.44 (0.16), residues: 1011 sheet: 1.30 (0.56), residues: 48 loop : -1.28 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 256 HIS 0.001 0.001 HIS B 296 PHE 0.012 0.001 PHE C 240 TYR 0.010 0.001 TYR A 373 ARG 0.006 0.000 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 131 time to evaluate : 1.096 Fit side-chains REVERT: A 330 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7653 (mt) REVERT: B 330 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7629 (mt) REVERT: B 442 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7644 (tp) REVERT: C 229 MET cc_start: 0.8884 (mtp) cc_final: 0.8639 (mtp) REVERT: C 274 GLU cc_start: 0.7205 (pm20) cc_final: 0.6939 (pm20) outliers start: 28 outliers final: 15 residues processed: 147 average time/residue: 1.1167 time to fit residues: 176.9808 Evaluate side-chains 148 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 130 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 441 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 91 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 57 optimal weight: 0.2980 chunk 76 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 ASN C 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10023 Z= 0.163 Angle : 0.473 5.494 13608 Z= 0.254 Chirality : 0.037 0.169 1725 Planarity : 0.003 0.033 1665 Dihedral : 3.668 17.329 1365 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 2.22 % Allowed : 19.58 % Favored : 78.21 % 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: 2.83 (0.23), residues: 1287 helix: 2.55 (0.16), residues: 1011 sheet: 1.34 (0.56), residues: 48 loop : -1.30 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 256 HIS 0.001 0.000 HIS B 296 PHE 0.009 0.001 PHE C 240 TYR 0.008 0.001 TYR A 373 ARG 0.006 0.000 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 1.145 Fit side-chains REVERT: A 330 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7660 (mt) REVERT: B 330 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7685 (mt) REVERT: B 442 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7573 (tp) REVERT: C 229 MET cc_start: 0.8855 (mtp) cc_final: 0.8605 (mtp) REVERT: C 274 GLU cc_start: 0.7220 (pm20) cc_final: 0.6962 (pm20) REVERT: C 432 ASP cc_start: 0.7550 (m-30) cc_final: 0.7073 (m-30) outliers start: 24 outliers final: 16 residues processed: 146 average time/residue: 1.1686 time to fit residues: 183.8098 Evaluate side-chains 151 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 441 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 11 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 312 ASN C 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10023 Z= 0.176 Angle : 0.488 6.598 13608 Z= 0.261 Chirality : 0.037 0.166 1725 Planarity : 0.004 0.035 1665 Dihedral : 3.684 17.175 1365 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 2.40 % Allowed : 19.76 % Favored : 77.84 % 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: 2.80 (0.23), residues: 1287 helix: 2.53 (0.16), residues: 1011 sheet: 1.33 (0.56), residues: 48 loop : -1.32 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 256 HIS 0.001 0.001 HIS B 296 PHE 0.011 0.001 PHE C 240 TYR 0.008 0.001 TYR A 373 ARG 0.007 0.000 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 1.189 Fit side-chains revert: symmetry clash REVERT: A 330 ILE cc_start: 0.7994 (OUTLIER) cc_final: 0.7681 (mt) REVERT: B 330 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7706 (mt) REVERT: B 442 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7611 (tp) REVERT: B 467 LYS cc_start: 0.7400 (OUTLIER) cc_final: 0.7073 (ptpt) REVERT: C 432 ASP cc_start: 0.7539 (m-30) cc_final: 0.7049 (m-30) outliers start: 26 outliers final: 17 residues processed: 144 average time/residue: 1.1458 time to fit residues: 177.6952 Evaluate side-chains 150 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 129 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 467 LYS Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 441 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.7980 chunk 115 optimal weight: 0.0980 chunk 119 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 122 optimal weight: 0.0060 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 312 ASN C 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10023 Z= 0.149 Angle : 0.470 6.918 13608 Z= 0.249 Chirality : 0.036 0.162 1725 Planarity : 0.003 0.039 1665 Dihedral : 3.589 16.763 1365 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 2.49 % Allowed : 19.85 % Favored : 77.65 % 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: 2.97 (0.23), residues: 1287 helix: 2.66 (0.16), residues: 1011 sheet: 1.31 (0.56), residues: 48 loop : -1.32 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 256 HIS 0.001 0.000 HIS B 296 PHE 0.008 0.001 PHE B 240 TYR 0.009 0.001 TYR A 373 ARG 0.007 0.000 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 130 time to evaluate : 1.059 Fit side-chains REVERT: A 330 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7674 (mt) REVERT: B 205 MET cc_start: 0.8472 (ptm) cc_final: 0.8210 (ptm) REVERT: B 330 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7566 (mt) REVERT: B 442 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7563 (tp) REVERT: C 432 ASP cc_start: 0.7518 (m-30) cc_final: 0.7045 (m-30) outliers start: 27 outliers final: 16 residues processed: 147 average time/residue: 1.2329 time to fit residues: 194.3728 Evaluate side-chains 148 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 129 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 441 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 128 optimal weight: 0.0870 chunk 118 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 79 optimal weight: 0.0970 chunk 62 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 overall best weight: 0.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 312 ASN C 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10023 Z= 0.171 Angle : 0.501 8.230 13608 Z= 0.263 Chirality : 0.037 0.162 1725 Planarity : 0.004 0.039 1665 Dihedral : 3.625 16.984 1365 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 2.22 % Allowed : 20.31 % Favored : 77.47 % 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: 2.89 (0.23), residues: 1287 helix: 2.60 (0.16), residues: 1011 sheet: 1.35 (0.55), residues: 48 loop : -1.32 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 256 HIS 0.001 0.001 HIS B 296 PHE 0.010 0.001 PHE C 240 TYR 0.010 0.001 TYR A 373 ARG 0.007 0.000 ARG A 315 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 130 time to evaluate : 1.171 Fit side-chains REVERT: A 330 ILE cc_start: 0.7849 (OUTLIER) cc_final: 0.7549 (mt) REVERT: B 205 MET cc_start: 0.8456 (ptm) cc_final: 0.8196 (ptm) REVERT: B 330 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7584 (mt) REVERT: B 442 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7613 (tp) REVERT: B 467 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.7079 (ptpt) REVERT: C 432 ASP cc_start: 0.7538 (m-30) cc_final: 0.7062 (m-30) outliers start: 24 outliers final: 16 residues processed: 144 average time/residue: 1.2083 time to fit residues: 186.8010 Evaluate side-chains 148 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 467 LYS Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 441 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 312 ASN C 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.168196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.110455 restraints weight = 10115.852| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.84 r_work: 0.3124 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10023 Z= 0.224 Angle : 0.537 8.969 13608 Z= 0.286 Chirality : 0.038 0.161 1725 Planarity : 0.004 0.037 1665 Dihedral : 3.813 17.492 1365 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.22 % Allowed : 20.31 % Favored : 77.47 % 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: 2.67 (0.23), residues: 1287 helix: 2.44 (0.16), residues: 1011 sheet: 1.32 (0.57), residues: 48 loop : -1.35 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 256 HIS 0.002 0.001 HIS B 296 PHE 0.013 0.002 PHE C 240 TYR 0.012 0.001 TYR A 373 ARG 0.007 0.001 ARG A 315 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3610.12 seconds wall clock time: 64 minutes 5.73 seconds (3845.73 seconds total)