Starting phenix.real_space_refine on Sun May 11 23:29:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zl3_60217/05_2025/8zl3_60217.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zl3_60217/05_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_60217/05_2025/8zl3_60217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zl3_60217/05_2025/8zl3_60217.map" model { file = "/net/cci-nas-00/data/ceres_data/8zl3_60217/05_2025/8zl3_60217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zl3_60217/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 5.61, per 1000 atoms: 0.66 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: 2.29 Conformation dependent library (CDL) restraints added in 999.5 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: 0.87 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: 2.25 Time building geometry restraints manager: 2.51 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: 0.05 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: 0.010 Normalize map: mean=0, sd=1: 1.200 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: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 22.360 Find NCS groups from input model: 0.290 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:11.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.190 ------------------------------------------------------------------------------- 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= 0.347 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 Details of bonding type rmsd hydrogen bonds : bond 0.15424 ( 543) hydrogen bonds : angle 5.38053 ( 1620) covalent geometry : bond 0.00765 ( 8774) covalent geometry : angle 1.20507 (11932) *********************** 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 : 0.920 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: 1.2690 time to fit residues: 112.8054 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 : 1.011 ------------------------------------------------------------------------------- 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 = 42)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.048752 restraints weight = 21072.229| |-----------------------------------------------------------------------------| r_work (start): 0.2661 rms_B_bonded: 2.89 r_work: 0.2531 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 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= 0.134 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 Details of bonding type rmsd hydrogen bonds : bond 0.05416 ( 543) hydrogen bonds : angle 4.26226 ( 1620) covalent geometry : bond 0.00277 ( 8774) covalent geometry : angle 0.56399 (11932) *********************** 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 : 0.967 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: 0.7820 (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: 1.2317 time to fit residues: 106.6367 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 : 0.870 ------------------------------------------------------------------------------- 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: 3.9990 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: 0.9990 chunk 78 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 9 optimal weight: 0.0370 chunk 40 optimal weight: 5.9990 overall best weight: 1.1664 ------------------------------------------------------------------------------- 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 = 0.3127 r_free = 0.3127 target = 0.069460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.049877 restraints weight = 21395.987| |-----------------------------------------------------------------------------| r_work (start): 0.2670 rms_B_bonded: 2.85 r_work: 0.2544 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8774 Z= 0.124 Angle : 0.526 5.895 11932 Z= 0.273 Chirality : 0.039 0.164 1384 Planarity : 0.005 0.042 1452 Dihedral : 8.582 127.799 1284 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.43 % Allowed : 7.60 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.26), residues: 1070 helix: 2.18 (0.19), residues: 786 sheet: None (None), residues: 0 loop : -0.95 (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 0.022 0.001 PHE A 251 TYR 0.032 0.001 TYR A 282 ARG 0.002 0.000 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.04791 ( 543) hydrogen bonds : angle 4.03544 ( 1620) covalent geometry : bond 0.00266 ( 8774) covalent geometry : angle 0.52574 (11932) *********************** 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 91 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.868 Fit side-chains REVERT: A 159 MET cc_start: 0.8942 (mmt) cc_final: 0.8724 (mmm) REVERT: A 363 ASP cc_start: 0.9090 (m-30) cc_final: 0.8818 (m-30) REVERT: A 369 ASP cc_start: 0.8074 (m-30) cc_final: 0.7762 (m-30) REVERT: B 328 ASP cc_start: 0.9050 (m-30) cc_final: 0.8711 (m-30) REVERT: B 363 ASP cc_start: 0.8692 (m-30) cc_final: 0.8344 (m-30) outliers start: 13 outliers final: 2 residues processed: 82 average time/residue: 1.2300 time to fit residues: 107.7404 Evaluate side-chains 76 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 316 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 6 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3131 r_free = 0.3131 target = 0.069590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.050044 restraints weight = 21280.844| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 2.83 r_work: 0.2556 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1402 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= 0.120 Angle : 0.523 8.054 11932 Z= 0.270 Chirality : 0.039 0.164 1384 Planarity : 0.005 0.047 1452 Dihedral : 8.440 126.325 1284 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.88 % Allowed : 9.25 % 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: 2.12 (0.26), residues: 1070 helix: 2.19 (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 0.007 0.001 TRP A 562 HIS 0.004 0.001 HIS B 335 PHE 0.021 0.001 PHE A 251 TYR 0.028 0.001 TYR A 282 ARG 0.002 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.04682 ( 543) hydrogen bonds : angle 3.98443 ( 1620) covalent geometry : bond 0.00257 ( 8774) covalent geometry : angle 0.52258 (11932) *********************** 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: 8 poor density : 74 time to evaluate : 0.912 Fit side-chains REVERT: A 159 MET cc_start: 0.8944 (mmt) cc_final: 0.8731 (mmm) REVERT: A 363 ASP cc_start: 0.9082 (m-30) cc_final: 0.8817 (m-30) REVERT: A 369 ASP cc_start: 0.8079 (m-30) cc_final: 0.7755 (m-30) REVERT: B 99 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8230 (mmt) REVERT: B 328 ASP cc_start: 0.9044 (m-30) cc_final: 0.8713 (m-30) REVERT: B 363 ASP cc_start: 0.8683 (m-30) cc_final: 0.8335 (m-30) outliers start: 8 outliers final: 2 residues processed: 77 average time/residue: 1.3043 time to fit residues: 106.9344 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 : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain B residue 99 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 17 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.3104 r_free = 0.3104 target = 0.068252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.048361 restraints weight = 21361.197| |-----------------------------------------------------------------------------| r_work (start): 0.2653 rms_B_bonded: 2.89 r_work: 0.2529 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 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 0.038 8774 Z= 0.156 Angle : 0.538 6.856 11932 Z= 0.278 Chirality : 0.040 0.172 1384 Planarity : 0.005 0.046 1452 Dihedral : 8.247 127.587 1284 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.77 % Allowed : 10.35 % 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: 2.13 (0.26), residues: 1070 helix: 2.21 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -0.93 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 562 HIS 0.005 0.001 HIS B 335 PHE 0.022 0.001 PHE A 251 TYR 0.026 0.001 TYR A 282 ARG 0.003 0.000 ARG A 371 Details of bonding type rmsd hydrogen bonds : bond 0.05003 ( 543) hydrogen bonds : angle 4.00462 ( 1620) covalent geometry : bond 0.00371 ( 8774) covalent geometry : angle 0.53829 (11932) *********************** 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 81 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.891 Fit side-chains REVERT: A 159 MET cc_start: 0.8930 (mmt) cc_final: 0.8724 (mmm) REVERT: A 363 ASP cc_start: 0.9007 (m-30) cc_final: 0.8748 (m-30) REVERT: A 369 ASP cc_start: 0.8066 (m-30) cc_final: 0.7829 (m-30) REVERT: B 328 ASP cc_start: 0.9060 (m-30) cc_final: 0.8724 (m-30) REVERT: B 363 ASP cc_start: 0.8685 (m-30) cc_final: 0.8309 (m-30) outliers start: 7 outliers final: 4 residues processed: 77 average time/residue: 1.2900 time to fit residues: 105.9018 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 : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 444 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 101 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 102 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 = 0.3118 r_free = 0.3118 target = 0.068802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.049098 restraints weight = 21077.858| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 2.85 r_work: 0.2543 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1441 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= 0.126 Angle : 0.522 6.932 11932 Z= 0.270 Chirality : 0.039 0.167 1384 Planarity : 0.005 0.046 1452 Dihedral : 8.133 126.750 1284 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.99 % Allowed : 10.35 % Favored : 88.66 % 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: 2.14 (0.26), residues: 1070 helix: 2.21 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -0.93 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 414 HIS 0.004 0.001 HIS B 335 PHE 0.020 0.001 PHE A 251 TYR 0.025 0.001 TYR A 282 ARG 0.004 0.000 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.04840 ( 543) hydrogen bonds : angle 3.96342 ( 1620) covalent geometry : bond 0.00275 ( 8774) covalent geometry : angle 0.52183 (11932) *********************** 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 : 0.888 Fit side-chains REVERT: A 159 MET cc_start: 0.8951 (mmt) cc_final: 0.8725 (mmm) REVERT: A 363 ASP cc_start: 0.9043 (m-30) cc_final: 0.8776 (m-30) REVERT: A 369 ASP cc_start: 0.8035 (m-30) cc_final: 0.7727 (m-30) REVERT: B 328 ASP cc_start: 0.9054 (m-30) cc_final: 0.8715 (m-30) REVERT: B 363 ASP cc_start: 0.8660 (m-30) cc_final: 0.8287 (m-30) outliers start: 9 outliers final: 3 residues processed: 79 average time/residue: 1.2173 time to fit residues: 102.7117 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 : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 316 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 102 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 89 optimal weight: 0.0170 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 35 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 overall best weight: 0.4820 ------------------------------------------------------------------------------- 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 = 0.3168 r_free = 0.3168 target = 0.071453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.051863 restraints weight = 21014.013| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 2.91 r_work: 0.2600 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8774 Z= 0.108 Angle : 0.506 7.757 11932 Z= 0.260 Chirality : 0.038 0.155 1384 Planarity : 0.005 0.047 1452 Dihedral : 7.606 119.148 1284 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.88 % Allowed : 10.24 % 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: 2.18 (0.26), residues: 1070 helix: 2.23 (0.18), 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 0.018 0.001 PHE A 268 TYR 0.026 0.001 TYR A 282 ARG 0.008 0.000 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 543) hydrogen bonds : angle 3.81264 ( 1620) covalent geometry : bond 0.00212 ( 8774) covalent geometry : angle 0.50601 (11932) *********************** 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 86 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.939 Fit side-chains REVERT: A 159 MET cc_start: 0.8915 (mmt) cc_final: 0.8700 (mmm) REVERT: A 261 ASN cc_start: 0.8604 (OUTLIER) cc_final: 0.8309 (t0) REVERT: A 363 ASP cc_start: 0.9054 (m-30) cc_final: 0.8781 (m-30) REVERT: B 363 ASP cc_start: 0.8624 (m-30) cc_final: 0.8291 (m-30) outliers start: 8 outliers final: 2 residues processed: 83 average time/residue: 1.2798 time to fit residues: 113.7399 Evaluate side-chains 75 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 308 VAL 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: 0.4980 chunk 20 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.3159 r_free = 0.3159 target = 0.070878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.051244 restraints weight = 21096.070| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 2.91 r_work: 0.2587 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 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 : 0.002 0.035 8774 Z= 0.113 Angle : 0.532 10.684 11932 Z= 0.267 Chirality : 0.039 0.161 1384 Planarity : 0.005 0.048 1452 Dihedral : 7.430 116.904 1284 Min Nonbonded Distance : 2.550 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: 2.23 (0.26), residues: 1070 helix: 2.28 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -0.88 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 562 HIS 0.003 0.001 HIS B 335 PHE 0.017 0.001 PHE A 251 TYR 0.025 0.001 TYR A 282 ARG 0.008 0.000 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.04095 ( 543) hydrogen bonds : angle 3.81516 ( 1620) covalent geometry : bond 0.00245 ( 8774) covalent geometry : angle 0.53172 (11932) *********************** 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 80 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.924 Fit side-chains REVERT: A 159 MET cc_start: 0.8916 (mmt) cc_final: 0.8704 (mmm) REVERT: A 363 ASP cc_start: 0.9056 (m-30) cc_final: 0.8783 (m-30) REVERT: B 328 ASP cc_start: 0.9051 (m-30) cc_final: 0.8562 (m-30) REVERT: B 363 ASP cc_start: 0.8618 (m-30) cc_final: 0.8277 (m-30) outliers start: 5 outliers final: 4 residues processed: 79 average time/residue: 1.3409 time to fit residues: 112.8288 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 : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 87 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 63 optimal weight: 0.2980 chunk 16 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.070465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.050772 restraints weight = 21095.251| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 2.90 r_work: 0.2576 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1765 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= 0.123 Angle : 0.535 10.260 11932 Z= 0.269 Chirality : 0.039 0.164 1384 Planarity : 0.005 0.049 1452 Dihedral : 7.360 115.483 1284 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: 2.25 (0.26), residues: 1070 helix: 2.29 (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 0.011 0.000 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.04237 ( 543) hydrogen bonds : angle 3.81788 ( 1620) covalent geometry : bond 0.00281 ( 8774) covalent geometry : angle 0.53507 (11932) *********************** 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 79 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.985 Fit side-chains REVERT: A 159 MET cc_start: 0.8918 (mmt) cc_final: 0.8706 (mmm) REVERT: A 295 MET cc_start: 0.7082 (OUTLIER) cc_final: 0.5941 (mpt) REVERT: A 363 ASP cc_start: 0.9053 (m-30) cc_final: 0.8770 (m-30) REVERT: B 328 ASP cc_start: 0.9095 (m-30) cc_final: 0.8585 (m-30) REVERT: B 363 ASP cc_start: 0.8614 (m-30) cc_final: 0.8275 (m-30) outliers start: 5 outliers final: 3 residues processed: 77 average time/residue: 1.3159 time to fit residues: 107.9471 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 : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 MET 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 42 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 105 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.069823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.049895 restraints weight = 21302.523| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 2.90 r_work: 0.2571 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1764 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= 0.138 Angle : 0.545 11.057 11932 Z= 0.274 Chirality : 0.040 0.182 1384 Planarity : 0.005 0.053 1452 Dihedral : 7.345 114.964 1284 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.77 % Allowed : 11.45 % Favored : 87.78 % 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: 2.28 (0.26), residues: 1070 helix: 2.31 (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 0.009 0.001 TRP A 562 HIS 0.004 0.001 HIS B 335 PHE 0.018 0.001 PHE A 251 TYR 0.024 0.001 TYR A 282 ARG 0.012 0.001 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.04354 ( 543) hydrogen bonds : angle 3.84243 ( 1620) covalent geometry : bond 0.00323 ( 8774) covalent geometry : angle 0.54533 (11932) ********************** 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 79 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: A 159 MET cc_start: 0.8952 (mmt) cc_final: 0.8740 (mmm) REVERT: A 295 MET cc_start: 0.7130 (OUTLIER) cc_final: 0.5976 (mpt) REVERT: A 363 ASP cc_start: 0.9041 (m-30) cc_final: 0.8759 (m-30) REVERT: B 328 ASP cc_start: 0.9110 (m-30) cc_final: 0.8593 (m-30) REVERT: B 363 ASP cc_start: 0.8623 (m-30) cc_final: 0.8284 (m-30) outliers start: 7 outliers final: 5 residues processed: 77 average time/residue: 1.3649 time to fit residues: 111.7575 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 : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 MET 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 Chi-restraints excluded: chain B residue 313 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 14 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3148 r_free = 0.3148 target = 0.070248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.050552 restraints weight = 21308.057| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 2.92 r_work: 0.2583 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1807 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= 0.119 Angle : 0.531 11.961 11932 Z= 0.267 Chirality : 0.039 0.170 1384 Planarity : 0.005 0.049 1452 Dihedral : 7.273 112.767 1284 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.77 % Allowed : 11.45 % Favored : 87.78 % 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: 2.29 (0.26), residues: 1070 helix: 2.32 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -0.85 (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 0.016 0.001 PHE A 251 TYR 0.024 0.001 TYR A 282 ARG 0.008 0.000 ARG A 371 Details of bonding type rmsd hydrogen bonds : bond 0.04296 ( 543) hydrogen bonds : angle 3.80160 ( 1620) covalent geometry : bond 0.00264 ( 8774) covalent geometry : angle 0.53142 (11932) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4443.60 seconds wall clock time: 77 minutes 32.42 seconds (4652.42 seconds total)