Starting phenix.real_space_refine on Fri Oct 10 18:50:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zl3_60217/10_2025/8zl3_60217.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zl3_60217/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8zl3_60217/10_2025/8zl3_60217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zl3_60217/10_2025/8zl3_60217.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zl3_60217/10_2025/8zl3_60217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zl3_60217/10_2025/8zl3_60217.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 2.24, per 1000 atoms: 0.26 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: 0.81 Conformation dependent library (CDL) restraints added in 328.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.26 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: 1.26 Time building geometry restraints manager: 1.03 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: 0.02 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: 0.930 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: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 8.670 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.010 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:6.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.310 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.001 ARG A 66 TYR 0.015 0.002 TYR B 111 PHE 0.026 0.002 PHE B 251 TRP 0.012 0.001 TRP B 562 HIS 0.009 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00765 ( 8774) covalent geometry : angle 1.20507 (11932) hydrogen bonds : bond 0.15424 ( 543) hydrogen bonds : angle 5.38053 ( 1620) *********************** 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 : 0.357 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: 0.6217 time to fit residues: 54.9678 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 : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 450 ASN A 485 ASN B 261 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.068452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.048809 restraints weight = 21314.425| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 2.85 r_work: 0.2539 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1091 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= 0.133 Angle : 0.561 6.313 11932 Z= 0.295 Chirality : 0.041 0.177 1384 Planarity : 0.005 0.047 1452 Dihedral : 9.120 122.634 1284 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.10 % Allowed : 5.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.25), residues: 1070 helix: 1.97 (0.18), residues: 786 sheet: None (None), residues: 0 loop : -0.91 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 312 TYR 0.039 0.001 TYR A 282 PHE 0.023 0.001 PHE A 251 TRP 0.009 0.001 TRP A 562 HIS 0.004 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8774) covalent geometry : angle 0.56092 (11932) hydrogen bonds : bond 0.05300 ( 543) hydrogen bonds : angle 4.24103 ( 1620) *********************** 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 89 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.340 Fit side-chains REVERT: A 363 ASP cc_start: 0.9102 (m-30) cc_final: 0.8835 (m-30) REVERT: A 369 ASP cc_start: 0.8232 (m-30) cc_final: 0.7869 (m-30) REVERT: B 328 ASP cc_start: 0.9075 (m-30) cc_final: 0.8705 (m-30) REVERT: B 363 ASP cc_start: 0.8710 (m-30) cc_final: 0.8360 (m-30) outliers start: 10 outliers final: 0 residues processed: 81 average time/residue: 0.6350 time to fit residues: 54.7250 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 : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 101 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.0470 chunk 37 optimal weight: 0.0970 chunk 38 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 4 optimal weight: 0.1980 overall best weight: 1.0680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.069090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.049488 restraints weight = 21065.984| |-----------------------------------------------------------------------------| r_work (start): 0.2675 rms_B_bonded: 2.85 r_work: 0.2551 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1297 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= 0.123 Angle : 0.523 5.989 11932 Z= 0.273 Chirality : 0.039 0.166 1384 Planarity : 0.005 0.049 1452 Dihedral : 8.684 126.457 1284 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.99 % Allowed : 7.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.26), residues: 1070 helix: 2.15 (0.18), residues: 786 sheet: None (None), residues: 0 loop : -0.94 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 312 TYR 0.031 0.001 TYR A 282 PHE 0.022 0.001 PHE A 251 TRP 0.008 0.001 TRP A 562 HIS 0.004 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 8774) covalent geometry : angle 0.52310 (11932) hydrogen bonds : bond 0.04827 ( 543) hydrogen bonds : angle 4.05961 ( 1620) *********************** 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: 9 poor density : 78 time to evaluate : 0.261 Fit side-chains REVERT: A 295 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.6178 (mpt) REVERT: A 363 ASP cc_start: 0.9099 (m-30) cc_final: 0.8825 (m-30) REVERT: A 369 ASP cc_start: 0.8144 (m-30) cc_final: 0.7834 (m-30) REVERT: B 328 ASP cc_start: 0.9059 (m-30) cc_final: 0.8696 (m-30) REVERT: B 363 ASP cc_start: 0.8703 (m-30) cc_final: 0.8346 (m-30) outliers start: 9 outliers final: 1 residues processed: 81 average time/residue: 0.6453 time to fit residues: 55.4950 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 : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 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 103 optimal weight: 5.9990 chunk 14 optimal weight: 0.0770 chunk 57 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 overall best weight: 0.9940 ------------------------------------------------------------------------------- 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 = 0.3133 r_free = 0.3133 target = 0.069781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.050112 restraints weight = 21432.791| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 2.93 r_work: 0.2552 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8774 Z= 0.118 Angle : 0.521 8.043 11932 Z= 0.269 Chirality : 0.039 0.164 1384 Planarity : 0.005 0.054 1452 Dihedral : 8.389 126.179 1284 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.88 % Allowed : 8.92 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (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 ARG 0.002 0.000 ARG A 66 TYR 0.028 0.001 TYR A 282 PHE 0.021 0.001 PHE A 251 TRP 0.009 0.001 TRP A 361 HIS 0.004 0.000 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8774) covalent geometry : angle 0.52064 (11932) hydrogen bonds : bond 0.04584 ( 543) hydrogen bonds : angle 3.96564 ( 1620) *********************** 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 83 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.324 Fit side-chains REVERT: A 363 ASP cc_start: 0.9085 (m-30) cc_final: 0.8813 (m-30) REVERT: A 369 ASP cc_start: 0.8062 (m-30) cc_final: 0.7736 (m-30) REVERT: B 328 ASP cc_start: 0.9042 (m-30) cc_final: 0.8674 (m-30) REVERT: B 363 ASP cc_start: 0.8678 (m-30) cc_final: 0.8328 (m-30) outliers start: 8 outliers final: 2 residues processed: 77 average time/residue: 0.6677 time to fit residues: 54.5519 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 : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 444 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 40 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 6 optimal weight: 0.0970 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 59 optimal weight: 0.0980 chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 = 0.3141 r_free = 0.3141 target = 0.070045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.050562 restraints weight = 21318.257| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 2.86 r_work: 0.2569 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1528 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 : 0.515 6.980 11932 Z= 0.266 Chirality : 0.039 0.164 1384 Planarity : 0.005 0.051 1452 Dihedral : 8.060 124.683 1284 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.88 % Allowed : 9.80 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.26), residues: 1070 helix: 2.22 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -0.90 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 312 TYR 0.026 0.001 TYR A 282 PHE 0.019 0.001 PHE A 251 TRP 0.008 0.001 TRP A 562 HIS 0.004 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 8774) covalent geometry : angle 0.51458 (11932) hydrogen bonds : bond 0.04492 ( 543) hydrogen bonds : angle 3.90646 ( 1620) *********************** 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 84 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.348 Fit side-chains REVERT: A 363 ASP cc_start: 0.9045 (m-30) cc_final: 0.8779 (m-30) REVERT: A 369 ASP cc_start: 0.8015 (m-30) cc_final: 0.7787 (m-30) REVERT: B 328 ASP cc_start: 0.9052 (m-30) cc_final: 0.8695 (m-30) REVERT: B 363 ASP cc_start: 0.8679 (m-30) cc_final: 0.8312 (m-30) outliers start: 8 outliers final: 2 residues processed: 78 average time/residue: 0.6524 time to fit residues: 54.1308 Evaluate side-chains 75 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 VAL 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 26 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.3147 r_free = 0.3147 target = 0.070364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.050804 restraints weight = 21051.842| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 2.85 r_work: 0.2580 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1646 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= 0.112 Angle : 0.511 7.812 11932 Z= 0.262 Chirality : 0.039 0.161 1384 Planarity : 0.005 0.050 1452 Dihedral : 7.711 120.702 1284 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.88 % Allowed : 10.46 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.26), residues: 1070 helix: 2.24 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -0.89 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 312 TYR 0.026 0.001 TYR A 282 PHE 0.017 0.001 PHE A 251 TRP 0.008 0.001 TRP A 562 HIS 0.003 0.000 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 8774) covalent geometry : angle 0.51085 (11932) hydrogen bonds : bond 0.04238 ( 543) hydrogen bonds : angle 3.83923 ( 1620) *********************** 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 85 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.337 Fit side-chains REVERT: A 261 ASN cc_start: 0.8635 (OUTLIER) cc_final: 0.8365 (t0) REVERT: A 363 ASP cc_start: 0.9025 (m-30) cc_final: 0.8756 (m-30) REVERT: A 369 ASP cc_start: 0.8032 (m-30) cc_final: 0.7812 (m-30) REVERT: B 328 ASP cc_start: 0.9054 (m-30) cc_final: 0.8696 (m-30) REVERT: B 363 ASP cc_start: 0.8625 (m-30) cc_final: 0.8271 (m-30) outliers start: 8 outliers final: 3 residues processed: 81 average time/residue: 0.6205 time to fit residues: 53.5371 Evaluate side-chains 78 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 328 ASP Chi-restraints excluded: chain A residue 444 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 80 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 44 optimal weight: 0.0770 chunk 54 optimal weight: 0.1980 chunk 61 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.5740 ------------------------------------------------------------------------------- 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 = 0.3163 r_free = 0.3163 target = 0.071071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.051426 restraints weight = 21197.183| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 2.92 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: 0.8315 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 : 0.002 0.036 8774 Z= 0.107 Angle : 0.505 8.084 11932 Z= 0.259 Chirality : 0.038 0.158 1384 Planarity : 0.005 0.049 1452 Dihedral : 7.500 117.319 1284 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.55 % Allowed : 11.01 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.25 (0.26), residues: 1070 helix: 2.28 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -0.84 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 312 TYR 0.025 0.001 TYR A 282 PHE 0.016 0.001 PHE B 251 TRP 0.008 0.001 TRP A 562 HIS 0.003 0.000 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 8774) covalent geometry : angle 0.50514 (11932) hydrogen bonds : bond 0.04014 ( 543) hydrogen bonds : angle 3.78498 ( 1620) *********************** 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 80 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.326 Fit side-chains REVERT: A 261 ASN cc_start: 0.8649 (OUTLIER) cc_final: 0.8388 (t0) REVERT: A 363 ASP cc_start: 0.9023 (m-30) cc_final: 0.8751 (m-30) REVERT: B 328 ASP cc_start: 0.9054 (m-30) cc_final: 0.8699 (m-30) REVERT: B 363 ASP cc_start: 0.8639 (m-30) cc_final: 0.8304 (m-30) outliers start: 5 outliers final: 6 residues processed: 79 average time/residue: 0.6779 time to fit residues: 56.7795 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 : 0.326 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 82 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 104 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- 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 = 0.3117 r_free = 0.3117 target = 0.068621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.048921 restraints weight = 21231.843| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 2.86 r_work: 0.2542 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8774 Z= 0.171 Angle : 0.550 10.094 11932 Z= 0.281 Chirality : 0.040 0.176 1384 Planarity : 0.005 0.048 1452 Dihedral : 7.650 118.051 1284 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.66 % Allowed : 10.79 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.010 0.000 ARG B 312 TYR 0.023 0.001 TYR A 282 PHE 0.021 0.001 PHE A 251 TRP 0.009 0.001 TRP A 562 HIS 0.006 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 8774) covalent geometry : angle 0.55011 (11932) hydrogen bonds : bond 0.04918 ( 543) hydrogen bonds : angle 3.90191 ( 1620) *********************** 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: 6 poor density : 74 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8600 (mmm) cc_final: 0.8386 (mmt) REVERT: A 363 ASP cc_start: 0.9018 (m-30) cc_final: 0.8733 (m-30) REVERT: A 369 ASP cc_start: 0.8011 (m-30) cc_final: 0.7799 (m-30) REVERT: A 372 ASN cc_start: 0.9010 (OUTLIER) cc_final: 0.8789 (t0) REVERT: B 363 ASP cc_start: 0.8621 (m-30) cc_final: 0.8276 (m-30) outliers start: 6 outliers final: 6 residues processed: 79 average time/residue: 0.6582 time to fit residues: 55.1717 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 : 0.327 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 313 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 34 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 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 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 = 0.3134 r_free = 0.3134 target = 0.069578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.049728 restraints weight = 21117.653| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 2.88 r_work: 0.2563 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1705 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= 0.118 Angle : 0.518 10.597 11932 Z= 0.265 Chirality : 0.039 0.165 1384 Planarity : 0.005 0.048 1452 Dihedral : 7.403 115.013 1284 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.55 % Allowed : 11.12 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.31 (0.26), residues: 1070 helix: 2.32 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -0.83 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 312 TYR 0.024 0.001 TYR A 282 PHE 0.016 0.001 PHE B 251 TRP 0.009 0.001 TRP A 562 HIS 0.004 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 8774) covalent geometry : angle 0.51837 (11932) hydrogen bonds : bond 0.04474 ( 543) hydrogen bonds : angle 3.81563 ( 1620) *********************** 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 81 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.350 Fit side-chains REVERT: A 363 ASP cc_start: 0.9029 (m-30) cc_final: 0.8743 (m-30) REVERT: A 369 ASP cc_start: 0.8004 (m-30) cc_final: 0.7800 (m-30) REVERT: A 372 ASN cc_start: 0.8819 (OUTLIER) cc_final: 0.8606 (t0) REVERT: B 328 ASP cc_start: 0.9082 (m-30) cc_final: 0.8582 (m-30) REVERT: B 363 ASP cc_start: 0.8614 (m-30) cc_final: 0.8275 (m-30) outliers start: 5 outliers final: 5 residues processed: 80 average time/residue: 0.6372 time to fit residues: 54.1453 Evaluate side-chains 80 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 29 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 36 optimal weight: 0.0050 chunk 43 optimal weight: 0.3980 chunk 46 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 88 optimal weight: 0.0970 chunk 1 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 overall best weight: 0.3992 ------------------------------------------------------------------------------- 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 = 0.3162 r_free = 0.3162 target = 0.071083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.051409 restraints weight = 20857.847| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 2.89 r_work: 0.2602 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1855 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= 0.109 Angle : 0.517 11.885 11932 Z= 0.262 Chirality : 0.038 0.156 1384 Planarity : 0.004 0.048 1452 Dihedral : 7.227 110.593 1284 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.66 % Allowed : 11.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.26), residues: 1070 helix: 2.33 (0.18), residues: 788 sheet: None (None), residues: 0 loop : -0.77 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 371 TYR 0.024 0.001 TYR A 282 PHE 0.017 0.001 PHE A 268 TRP 0.009 0.001 TRP B 562 HIS 0.003 0.000 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 8774) covalent geometry : angle 0.51653 (11932) hydrogen bonds : bond 0.03996 ( 543) hydrogen bonds : angle 3.74416 ( 1620) ********************** 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 82 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.337 Fit side-chains REVERT: A 363 ASP cc_start: 0.9044 (m-30) cc_final: 0.8766 (m-30) REVERT: A 369 ASP cc_start: 0.7982 (m-30) cc_final: 0.7769 (m-30) REVERT: B 328 ASP cc_start: 0.9102 (m-30) cc_final: 0.8601 (m-30) REVERT: B 363 ASP cc_start: 0.8619 (m-30) cc_final: 0.8287 (m-30) outliers start: 6 outliers final: 4 residues processed: 81 average time/residue: 0.6416 time to fit residues: 55.2785 Evaluate side-chains 78 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 33 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 59 optimal weight: 0.0020 chunk 57 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- 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 = 0.3172 r_free = 0.3172 target = 0.071544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.051923 restraints weight = 21093.474| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 2.91 r_work: 0.2604 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1951 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= 0.106 Angle : 0.527 11.576 11932 Z= 0.263 Chirality : 0.038 0.155 1384 Planarity : 0.005 0.050 1452 Dihedral : 7.087 106.673 1284 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.44 % Allowed : 11.67 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.41 (0.26), residues: 1070 helix: 2.37 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -0.70 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 312 TYR 0.025 0.001 TYR A 282 PHE 0.017 0.001 PHE A 268 TRP 0.009 0.001 TRP A 562 HIS 0.002 0.000 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 8774) covalent geometry : angle 0.52730 (11932) hydrogen bonds : bond 0.03858 ( 543) hydrogen bonds : angle 3.72467 ( 1620) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2272.88 seconds wall clock time: 39 minutes 37.43 seconds (2377.43 seconds total)