Starting phenix.real_space_refine on Thu Mar 13 02:33:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zl3_60217/03_2025/8zl3_60217.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zl3_60217/03_2025/8zl3_60217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zl3_60217/03_2025/8zl3_60217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zl3_60217/03_2025/8zl3_60217.map" model { file = "/net/cci-nas-00/data/ceres_data/8zl3_60217/03_2025/8zl3_60217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zl3_60217/03_2025/8zl3_60217.cif" } resolution = 2.9 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= 0.003 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 96 5.16 5 C 5672 2.51 5 N 1334 2.21 5 O 1446 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8550 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4183 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 33, 'TRANS': 505} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 4183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4183 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 33, 'TRANS': 505} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 92 Unusual residues: {'4DS': 1, 'NAG': 1, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 92 Unusual residues: {'4DS': 1, 'NAG': 1, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.38, per 1000 atoms: 0.63 Number of scatterers: 8550 At special positions: 0 Unit cell: (90.2312, 99.5949, 108.107, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 2 15.00 O 1446 8.00 N 1334 7.00 C 5672 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 - 3.00 Amino acid : True - 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: 2.23 Conformation dependent library (CDL) restraints added in 942.8 milliseconds 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 0 sheets defined 81.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 33 through 40 removed outlier: 3.552A pdb=" N PHE A 37 " --> pdb=" O CYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 54 removed outlier: 3.568A pdb=" N LEU A 44 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 54 through 60 removed outlier: 3.748A pdb=" N ASN A 60 " --> pdb=" O VAL A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 81 removed outlier: 3.873A pdb=" N ARG A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 89 Processing helix chain 'A' and resid 90 through 100 removed outlier: 4.113A pdb=" N VAL A 94 " --> pdb=" O MET A 90 " (cutoff:3.500A) Proline residue: A 97 - end of helix Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.647A pdb=" N TYR A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 132 removed outlier: 3.802A pdb=" N CYS A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 147 removed outlier: 3.926A pdb=" N ARG A 137 " --> pdb=" O ASN A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 166 Processing helix chain 'A' and resid 169 through 191 Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 220 through 239 removed outlier: 4.139A pdb=" N CYS A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 244 removed outlier: 7.045A pdb=" N ILE A 243 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 259 removed outlier: 3.810A pdb=" N LEU A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 295 Proline residue: A 277 - end of helix Processing helix chain 'A' and resid 301 through 314 removed outlier: 3.869A pdb=" N ARG A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY A 311 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ARG A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 329 Processing helix chain 'A' and resid 333 through 352 Processing helix chain 'A' and resid 372 through 386 removed outlier: 4.657A pdb=" N THR A 376 " --> pdb=" O ASN A 372 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 398 Processing helix chain 'A' and resid 413 through 421 Processing helix chain 'A' and resid 424 through 443 removed outlier: 4.172A pdb=" N GLY A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 452 Processing helix chain 'A' and resid 453 through 458 removed outlier: 4.069A pdb=" N VAL A 457 " --> pdb=" O GLY A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 476 removed outlier: 3.555A pdb=" N ALA A 476 " --> pdb=" O VAL A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 498 Proline residue: A 489 - end of helix Processing helix chain 'A' and resid 501 through 513 removed outlier: 3.975A pdb=" N LEU A 505 " --> pdb=" O HIS A 501 " (cutoff:3.500A) Proline residue: A 508 - end of helix Processing helix chain 'A' and resid 523 through 533 Processing helix chain 'A' and resid 536 through 544 removed outlier: 3.641A pdb=" N MET A 540 " --> pdb=" O ARG A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 567 removed outlier: 3.677A pdb=" N THR A 548 " --> pdb=" O GLY A 544 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N LEU A 564 " --> pdb=" O GLN A 560 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 566 " --> pdb=" O TRP A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 583 Processing helix chain 'B' and resid 34 through 40 Processing helix chain 'B' and resid 40 through 60 removed outlier: 3.575A pdb=" N LEU B 44 " --> pdb=" O HIS B 40 " (cutoff:3.500A) Proline residue: B 50 - end of helix Proline residue: B 55 - end of helix removed outlier: 3.910A pdb=" N ASN B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 81 removed outlier: 3.707A pdb=" N CYS B 67 " --> pdb=" O ALA B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 89 Processing helix chain 'B' and resid 90 through 100 removed outlier: 4.095A pdb=" N VAL B 94 " --> pdb=" O MET B 90 " (cutoff:3.500A) Proline residue: B 97 - end of helix Processing helix chain 'B' and resid 103 through 109 Processing helix chain 'B' and resid 113 through 132 removed outlier: 3.780A pdb=" N CYS B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 147 removed outlier: 3.930A pdb=" N ARG B 137 " --> pdb=" O ASN B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 166 Processing helix chain 'B' and resid 169 through 191 Proline residue: B 179 - end of helix Processing helix chain 'B' and resid 220 through 238 Processing helix chain 'B' and resid 239 through 241 No H-bonds generated for 'chain 'B' and resid 239 through 241' Processing helix chain 'B' and resid 245 through 259 removed outlier: 3.830A pdb=" N LEU B 249 " --> pdb=" O THR B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 296 Proline residue: B 277 - end of helix removed outlier: 3.564A pdb=" N GLY B 296 " --> pdb=" O TRP B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 315 removed outlier: 4.589A pdb=" N GLU B 307 " --> pdb=" O LYS B 303 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALA B 315 " --> pdb=" O GLY B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 330 removed outlier: 3.823A pdb=" N ASP B 323 " --> pdb=" O LYS B 319 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN B 324 " --> pdb=" O LYS B 320 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 329 " --> pdb=" O ARG B 325 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY B 330 " --> pdb=" O TYR B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 352 Processing helix chain 'B' and resid 372 through 386 removed outlier: 4.047A pdb=" N THR B 376 " --> pdb=" O ASN B 372 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE B 384 " --> pdb=" O VAL B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 392 No H-bonds generated for 'chain 'B' and resid 390 through 392' Processing helix chain 'B' and resid 393 through 398 Processing helix chain 'B' and resid 413 through 421 Processing helix chain 'B' and resid 424 through 443 removed outlier: 3.602A pdb=" N LEU B 428 " --> pdb=" O GLY B 424 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY B 443 " --> pdb=" O SER B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 453 removed outlier: 3.726A pdb=" N ILE B 453 " --> pdb=" O GLY B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 458 removed outlier: 4.414A pdb=" N VAL B 457 " --> pdb=" O GLY B 454 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 458 " --> pdb=" O LEU B 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 454 through 458' Processing helix chain 'B' and resid 459 through 476 Processing helix chain 'B' and resid 479 through 499 Proline residue: B 489 - end of helix Processing helix chain 'B' and resid 501 through 513 removed outlier: 4.025A pdb=" N LEU B 505 " --> pdb=" O HIS B 501 " (cutoff:3.500A) Proline residue: B 508 - end of helix Processing helix chain 'B' and resid 523 through 533 Processing helix chain 'B' and resid 536 through 567 removed outlier: 4.835A pdb=" N GLY B 546 " --> pdb=" O ILE B 542 " (cutoff:3.500A) Proline residue: B 547 - end of helix removed outlier: 5.157A pdb=" N LEU B 564 " --> pdb=" O GLN B 560 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL B 565 " --> pdb=" O THR B 561 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 566 " --> pdb=" O TRP B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 584 543 hydrogen bonds defined for protein. 1620 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: 2.12 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1296 1.32 - 1.44: 2330 1.44 - 1.56: 4990 1.56 - 1.69: 8 1.69 - 1.81: 150 Bond restraints: 8774 Sorted by residual: bond pdb=" CBA 4DS A 603 " pdb=" NAZ 4DS A 603 " ideal model delta sigma weight residual 1.170 1.315 -0.145 2.00e-02 2.50e+03 5.28e+01 bond pdb=" CAT 4DS B 603 " pdb=" NAS 4DS B 603 " ideal model delta sigma weight residual 1.170 1.315 -0.145 2.00e-02 2.50e+03 5.26e+01 bond pdb=" CAT 4DS A 603 " pdb=" NAS 4DS A 603 " ideal model delta sigma weight residual 1.170 1.315 -0.145 2.00e-02 2.50e+03 5.25e+01 bond pdb=" CBA 4DS B 603 " pdb=" NAZ 4DS B 603 " ideal model delta sigma weight residual 1.170 1.313 -0.143 2.00e-02 2.50e+03 5.14e+01 bond pdb=" N ILE A 483 " pdb=" CA ILE A 483 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.68e+00 ... (remaining 8769 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.84: 11928 10.84 - 21.68: 0 21.68 - 32.52: 0 32.52 - 43.36: 0 43.36 - 54.19: 4 Bond angle restraints: 11932 Sorted by residual: angle pdb=" CAG 4DS B 603 " pdb=" NAZ 4DS B 603 " pdb=" CBA 4DS B 603 " ideal model delta sigma weight residual 177.62 123.43 54.19 3.00e+00 1.11e-01 3.26e+02 angle pdb=" CAP 4DS A 603 " pdb=" NAS 4DS A 603 " pdb=" CAT 4DS A 603 " ideal model delta sigma weight residual 180.00 125.92 54.08 3.00e+00 1.11e-01 3.25e+02 angle pdb=" CAP 4DS B 603 " pdb=" NAS 4DS B 603 " pdb=" CAT 4DS B 603 " ideal model delta sigma weight residual 180.00 127.37 52.63 3.00e+00 1.11e-01 3.08e+02 angle pdb=" CAG 4DS A 603 " pdb=" NAZ 4DS A 603 " pdb=" CBA 4DS A 603 " ideal model delta sigma weight residual 177.62 124.99 52.63 3.00e+00 1.11e-01 3.08e+02 angle pdb=" C ILE A 486 " pdb=" N ILE A 487 " pdb=" CA ILE A 487 " ideal model delta sigma weight residual 121.84 118.09 3.75 1.13e+00 7.83e-01 1.10e+01 ... (remaining 11927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.88: 5033 24.88 - 49.75: 164 49.75 - 74.63: 7 74.63 - 99.51: 0 99.51 - 124.38: 4 Dihedral angle restraints: 5208 sinusoidal: 2084 harmonic: 3124 Sorted by residual: dihedral pdb=" CA ARG A 371 " pdb=" C ARG A 371 " pdb=" N ASN A 372 " pdb=" CA ASN A 372 " ideal model delta harmonic sigma weight residual 180.00 154.48 25.52 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" N1 PTY B 601 " pdb=" C2 PTY B 601 " pdb=" C3 PTY B 601 " pdb=" O11 PTY B 601 " ideal model delta sinusoidal sigma weight residual 65.33 -59.05 124.38 1 3.00e+01 1.11e-03 1.67e+01 dihedral pdb=" N1 PTY A 601 " pdb=" C2 PTY A 601 " pdb=" C3 PTY A 601 " pdb=" O11 PTY A 601 " ideal model delta sinusoidal sigma weight residual 65.33 -56.50 121.83 1 3.00e+01 1.11e-03 1.63e+01 ... (remaining 5205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1071 0.051 - 0.101: 256 0.101 - 0.152: 48 0.152 - 0.202: 6 0.202 - 0.253: 3 Chirality restraints: 1384 Sorted by residual: chirality pdb=" CA TYR B 282 " pdb=" N TYR B 282 " pdb=" C TYR B 282 " pdb=" CB TYR B 282 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA TYR A 282 " pdb=" N TYR A 282 " pdb=" C TYR A 282 " pdb=" CB TYR A 282 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" C6 PTY B 601 " pdb=" C1 PTY B 601 " pdb=" C5 PTY B 601 " pdb=" O7 PTY B 601 " both_signs ideal model delta sigma weight residual False 2.49 2.26 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1381 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAJ 4DS B 603 " -0.108 2.00e-02 2.50e+03 1.11e-01 1.23e+02 pdb=" CAK 4DS B 603 " 0.097 2.00e-02 2.50e+03 pdb=" CAL 4DS B 603 " 0.124 2.00e-02 2.50e+03 pdb=" CAM 4DS B 603 " -0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAJ 4DS A 603 " 0.106 2.00e-02 2.50e+03 1.10e-01 1.20e+02 pdb=" CAK 4DS A 603 " -0.096 2.00e-02 2.50e+03 pdb=" CAL 4DS A 603 " -0.122 2.00e-02 2.50e+03 pdb=" CAM 4DS A 603 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 421 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO A 422 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 422 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 422 " 0.036 5.00e-02 4.00e+02 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 3000 2.86 - 3.37: 8687 3.37 - 3.88: 13261 3.88 - 4.39: 14497 4.39 - 4.90: 25879 Nonbonded interactions: 65324 Sorted by model distance: nonbonded pdb=" OH TYR B 350 " pdb=" OG1 THR B 376 " model vdw 2.350 3.040 nonbonded pdb=" O ASN A 372 " pdb=" ND2 ASN A 372 " model vdw 2.384 3.120 nonbonded pdb=" OD1 ASP B 323 " pdb=" N GLN B 324 " model vdw 2.406 3.120 nonbonded pdb=" O PRO B 404 " pdb=" OG1 THR B 405 " model vdw 2.428 3.040 nonbonded pdb=" O ASN A 261 " pdb=" ND2 ASN A 261 " model vdw 2.429 3.120 ... (remaining 65319 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.130 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.490 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:12.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 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 : 0.008 0.145 8774 Z= 0.523 Angle : 1.205 54.195 11932 Z= 0.499 Chirality : 0.046 0.253 1384 Planarity : 0.007 0.111 1452 Dihedral : 12.002 124.384 3196 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.11 % Allowed : 0.11 % Favored : 99.78 % 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: 1.54 (0.25), residues: 1070 helix: 1.78 (0.18), residues: 762 sheet: None (None), residues: 0 loop : -0.90 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 562 HIS 0.009 0.001 HIS B 335 PHE 0.026 0.002 PHE B 251 TYR 0.015 0.002 TYR B 111 ARG 0.004 0.001 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 0.899 Fit side-chains REVERT: A 159 MET cc_start: 0.9050 (mmt) cc_final: 0.8745 (mmm) REVERT: A 363 ASP cc_start: 0.8981 (m-30) cc_final: 0.8742 (m-30) REVERT: A 369 ASP cc_start: 0.8318 (m-30) cc_final: 0.7960 (m-30) REVERT: B 328 ASP cc_start: 0.8972 (m-30) cc_final: 0.8588 (m-30) REVERT: B 363 ASP cc_start: 0.8690 (m-30) cc_final: 0.8363 (m-30) outliers start: 1 outliers final: 0 residues processed: 83 average time/residue: 1.3091 time to fit residues: 115.8253 Evaluate side-chains 71 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.4980 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 83 optimal weight: 0.3980 chunk 32 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 485 ASN B 261 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.068326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.048751 restraints weight = 21072.226| |-----------------------------------------------------------------------------| r_work (start): 0.2661 rms_B_bonded: 2.90 r_work: 0.2531 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8774 Z= 0.184 Angle : 0.564 6.721 11932 Z= 0.296 Chirality : 0.041 0.177 1384 Planarity : 0.005 0.046 1452 Dihedral : 9.145 122.914 1284 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.21 % Allowed : 5.18 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.25), residues: 1070 helix: 1.98 (0.18), residues: 786 sheet: None (None), residues: 0 loop : -0.91 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 562 HIS 0.004 0.001 HIS B 335 PHE 0.024 0.001 PHE A 251 TYR 0.037 0.001 TYR A 282 ARG 0.005 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.909 Fit side-chains REVERT: A 363 ASP cc_start: 0.9086 (m-30) cc_final: 0.8811 (m-30) REVERT: A 369 ASP cc_start: 0.8180 (m-30) cc_final: 0.7819 (m-30) REVERT: B 328 ASP cc_start: 0.9069 (m-30) cc_final: 0.8730 (m-30) REVERT: B 363 ASP cc_start: 0.8696 (m-30) cc_final: 0.8352 (m-30) outliers start: 11 outliers final: 0 residues processed: 81 average time/residue: 1.2607 time to fit residues: 109.1162 Evaluate side-chains 74 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 78 optimal weight: 6.9990 chunk 53 optimal weight: 0.0770 chunk 60 optimal weight: 2.9990 chunk 9 optimal weight: 0.0670 chunk 40 optimal weight: 5.9990 overall best weight: 1.3680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.068587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.048941 restraints weight = 21502.553| |-----------------------------------------------------------------------------| r_work (start): 0.2655 rms_B_bonded: 2.87 r_work: 0.2528 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8774 Z= 0.187 Angle : 0.532 5.984 11932 Z= 0.277 Chirality : 0.040 0.170 1384 Planarity : 0.005 0.045 1452 Dihedral : 8.725 125.584 1284 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.21 % Allowed : 7.27 % Favored : 91.52 % 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: 2.02 (0.26), residues: 1070 helix: 2.13 (0.18), residues: 786 sheet: None (None), residues: 0 loop : -0.96 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 562 HIS 0.004 0.001 HIS B 335 PHE 0.023 0.001 PHE A 251 TYR 0.031 0.001 TYR A 282 ARG 0.003 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.872 Fit side-chains REVERT: A 295 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.6197 (mpt) REVERT: A 363 ASP cc_start: 0.9115 (m-30) cc_final: 0.8859 (m-30) REVERT: A 369 ASP cc_start: 0.8167 (m-30) cc_final: 0.7864 (m-30) REVERT: B 328 ASP cc_start: 0.9063 (m-30) cc_final: 0.8720 (m-30) REVERT: B 363 ASP cc_start: 0.8705 (m-30) cc_final: 0.8358 (m-30) outliers start: 11 outliers final: 2 residues processed: 80 average time/residue: 1.2667 time to fit residues: 108.0312 Evaluate side-chains 77 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 444 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 6 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 chunk 53 optimal weight: 0.0010 chunk 51 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.070811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.051173 restraints weight = 21216.902| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 2.92 r_work: 0.2576 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8774 Z= 0.146 Angle : 0.514 9.520 11932 Z= 0.264 Chirality : 0.039 0.157 1384 Planarity : 0.005 0.047 1452 Dihedral : 8.282 125.027 1284 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.66 % Allowed : 9.47 % Favored : 89.87 % 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: 2.13 (0.26), residues: 1070 helix: 2.20 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -0.92 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 562 HIS 0.003 0.000 HIS A 335 PHE 0.019 0.001 PHE A 251 TYR 0.030 0.001 TYR A 282 ARG 0.002 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 1.191 Fit side-chains REVERT: A 363 ASP cc_start: 0.9072 (m-30) cc_final: 0.8799 (m-30) REVERT: A 369 ASP cc_start: 0.8098 (m-30) cc_final: 0.7780 (m-30) REVERT: B 328 ASP cc_start: 0.9052 (m-30) cc_final: 0.8723 (m-30) REVERT: B 363 ASP cc_start: 0.8674 (m-30) cc_final: 0.8326 (m-30) outliers start: 6 outliers final: 0 residues processed: 79 average time/residue: 1.7687 time to fit residues: 149.0576 Evaluate side-chains 73 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 17 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.070237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.050756 restraints weight = 21069.295| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 2.83 r_work: 0.2574 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8774 Z= 0.182 Angle : 0.512 7.225 11932 Z= 0.263 Chirality : 0.039 0.164 1384 Planarity : 0.005 0.047 1452 Dihedral : 8.009 123.866 1284 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.55 % Allowed : 10.57 % Favored : 88.88 % 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: 2.16 (0.26), residues: 1070 helix: 2.23 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -0.94 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 562 HIS 0.004 0.001 HIS B 335 PHE 0.019 0.001 PHE A 251 TYR 0.026 0.001 TYR A 282 ARG 0.006 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.884 Fit side-chains REVERT: A 261 ASN cc_start: 0.8690 (OUTLIER) cc_final: 0.8400 (t0) REVERT: A 363 ASP cc_start: 0.9017 (m-30) cc_final: 0.8756 (m-30) REVERT: A 369 ASP cc_start: 0.8086 (m-30) cc_final: 0.7861 (m-30) REVERT: B 328 ASP cc_start: 0.9059 (m-30) cc_final: 0.8723 (m-30) REVERT: B 363 ASP cc_start: 0.8651 (m-30) cc_final: 0.8288 (m-30) outliers start: 5 outliers final: 2 residues processed: 78 average time/residue: 1.4068 time to fit residues: 116.6005 Evaluate side-chains 76 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 372 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 101 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 5 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 79 optimal weight: 0.0570 chunk 56 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 485 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.071399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.051738 restraints weight = 20963.091| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 2.91 r_work: 0.2593 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8774 Z= 0.140 Angle : 0.496 6.873 11932 Z= 0.255 Chirality : 0.038 0.157 1384 Planarity : 0.004 0.047 1452 Dihedral : 7.690 119.676 1284 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.99 % Allowed : 10.24 % Favored : 88.77 % 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: 2.18 (0.26), residues: 1070 helix: 2.25 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -0.92 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 562 HIS 0.003 0.000 HIS B 335 PHE 0.017 0.001 PHE A 268 TYR 0.026 0.001 TYR A 282 ARG 0.005 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.952 Fit side-chains REVERT: A 261 ASN cc_start: 0.8612 (OUTLIER) cc_final: 0.8334 (t0) REVERT: A 363 ASP cc_start: 0.9025 (m-30) cc_final: 0.8757 (m-30) REVERT: B 328 ASP cc_start: 0.9051 (m-30) cc_final: 0.8718 (m-30) REVERT: B 363 ASP cc_start: 0.8635 (m-30) cc_final: 0.8286 (m-30) outliers start: 9 outliers final: 3 residues processed: 81 average time/residue: 1.3629 time to fit residues: 117.7544 Evaluate side-chains 77 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain B residue 332 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 102 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 69 optimal weight: 0.0970 chunk 35 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 84 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.071510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.051886 restraints weight = 21040.904| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 2.93 r_work: 0.2602 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8774 Z= 0.141 Angle : 0.496 8.448 11932 Z= 0.254 Chirality : 0.038 0.157 1384 Planarity : 0.004 0.047 1452 Dihedral : 7.357 114.646 1284 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.88 % Allowed : 10.90 % Favored : 88.22 % 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: 2.25 (0.26), residues: 1070 helix: 2.29 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -0.87 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 562 HIS 0.002 0.000 HIS B 335 PHE 0.016 0.001 PHE A 268 TYR 0.024 0.001 TYR A 282 ARG 0.003 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.942 Fit side-chains REVERT: A 261 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8362 (t0) REVERT: A 363 ASP cc_start: 0.9017 (m-30) cc_final: 0.8751 (m-30) REVERT: B 363 ASP cc_start: 0.8639 (m-30) cc_final: 0.8306 (m-30) outliers start: 8 outliers final: 4 residues processed: 83 average time/residue: 1.3423 time to fit residues: 118.7012 Evaluate side-chains 78 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain B residue 220 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 83 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.070970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.051266 restraints weight = 21106.644| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 2.93 r_work: 0.2579 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8774 Z= 0.190 Angle : 0.518 9.522 11932 Z= 0.264 Chirality : 0.039 0.164 1384 Planarity : 0.005 0.048 1452 Dihedral : 7.280 113.418 1284 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.55 % Allowed : 11.45 % Favored : 88.00 % 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: 2.29 (0.26), residues: 1070 helix: 2.32 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -0.86 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 562 HIS 0.004 0.001 HIS B 335 PHE 0.017 0.001 PHE A 251 TYR 0.024 0.001 TYR A 282 ARG 0.010 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.886 Fit side-chains REVERT: A 363 ASP cc_start: 0.9019 (m-30) cc_final: 0.8747 (m-30) REVERT: B 328 ASP cc_start: 0.9052 (m-30) cc_final: 0.8580 (m-30) REVERT: B 363 ASP cc_start: 0.8624 (m-30) cc_final: 0.8275 (m-30) outliers start: 5 outliers final: 5 residues processed: 78 average time/residue: 1.2987 time to fit residues: 107.9093 Evaluate side-chains 78 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain B residue 220 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 87 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 8 optimal weight: 0.0870 chunk 67 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 0.0040 overall best weight: 0.6170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 372 ASN B 261 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.071460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.051839 restraints weight = 21011.980| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 2.93 r_work: 0.2602 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8774 Z= 0.142 Angle : 0.503 11.290 11932 Z= 0.255 Chirality : 0.038 0.157 1384 Planarity : 0.004 0.049 1452 Dihedral : 7.165 109.828 1284 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.66 % Allowed : 11.34 % Favored : 88.00 % 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: 2.31 (0.26), residues: 1070 helix: 2.33 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -0.82 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 562 HIS 0.003 0.000 HIS B 335 PHE 0.016 0.001 PHE A 268 TYR 0.024 0.001 TYR A 282 ARG 0.009 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.949 Fit side-chains REVERT: A 363 ASP cc_start: 0.9055 (m-30) cc_final: 0.8788 (m-30) REVERT: B 328 ASP cc_start: 0.9082 (m-30) cc_final: 0.8588 (m-30) REVERT: B 363 ASP cc_start: 0.8639 (m-30) cc_final: 0.8309 (m-30) outliers start: 6 outliers final: 4 residues processed: 76 average time/residue: 1.3313 time to fit residues: 107.8633 Evaluate side-chains 75 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain B residue 220 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 42 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 59 optimal weight: 0.2980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.071253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.051585 restraints weight = 21031.275| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 2.93 r_work: 0.2598 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8774 Z= 0.161 Angle : 0.505 11.718 11932 Z= 0.256 Chirality : 0.039 0.160 1384 Planarity : 0.005 0.049 1452 Dihedral : 7.054 107.762 1284 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.44 % Allowed : 11.45 % Favored : 88.11 % 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: 2.35 (0.26), residues: 1070 helix: 2.35 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -0.81 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 562 HIS 0.003 0.000 HIS B 335 PHE 0.016 0.001 PHE A 268 TYR 0.024 0.001 TYR A 282 ARG 0.007 0.000 ARG A 371 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 1.003 Fit side-chains REVERT: A 266 MET cc_start: 0.9220 (ttm) cc_final: 0.9017 (ttm) REVERT: A 363 ASP cc_start: 0.9055 (m-30) cc_final: 0.8778 (m-30) REVERT: B 328 ASP cc_start: 0.9085 (m-30) cc_final: 0.8579 (m-30) REVERT: B 363 ASP cc_start: 0.8631 (m-30) cc_final: 0.8285 (m-30) outliers start: 4 outliers final: 3 residues processed: 75 average time/residue: 1.4134 time to fit residues: 112.8741 Evaluate side-chains 74 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain B residue 220 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 14 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 16 optimal weight: 0.0070 chunk 7 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 93 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.071503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.051827 restraints weight = 21283.784| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 2.93 r_work: 0.2598 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8774 Z= 0.152 Angle : 0.504 11.668 11932 Z= 0.255 Chirality : 0.038 0.159 1384 Planarity : 0.004 0.049 1452 Dihedral : 7.009 106.258 1284 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.88 % Allowed : 11.01 % Favored : 88.11 % 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: 2.36 (0.26), residues: 1070 helix: 2.36 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -0.80 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 562 HIS 0.003 0.000 HIS B 335 PHE 0.015 0.001 PHE A 268 TYR 0.025 0.001 TYR A 282 ARG 0.007 0.000 ARG A 371 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4852.13 seconds wall clock time: 85 minutes 37.57 seconds (5137.57 seconds total)