Starting phenix.real_space_refine on Thu Mar 13 01:28:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zl6_60220/03_2025/8zl6_60220.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zl6_60220/03_2025/8zl6_60220.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zl6_60220/03_2025/8zl6_60220.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zl6_60220/03_2025/8zl6_60220.map" model { file = "/net/cci-nas-00/data/ceres_data/8zl6_60220/03_2025/8zl6_60220.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zl6_60220/03_2025/8zl6_60220.cif" } resolution = 2.8 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= 0.001 sd= 0.015 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 86 5.16 5 C 5652 2.51 5 N 1344 2.21 5 O 1424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8508 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4190 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 33, 'TRANS': 505} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4190 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 33, 'TRANS': 505} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'NAG': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'NAG': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.43, per 1000 atoms: 0.64 Number of scatterers: 8508 At special positions: 0 Unit cell: (91.9337, 104.702, 84.2726, 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 86 16.00 P 2 15.00 O 1424 8.00 N 1344 7.00 C 5652 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: 2.10 Conformation dependent library (CDL) restraints added in 993.8 milliseconds 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 81.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 32 through 53 removed outlier: 3.520A pdb=" N PHE A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE A 37 " --> pdb=" O CYS A 33 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LYS A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLY A 43 " --> pdb=" O ASN A 39 " (cutoff:3.500A) Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 53 through 60 removed outlier: 4.149A pdb=" N MET A 57 " --> pdb=" O CYS A 53 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN A 60 " --> pdb=" O VAL A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 81 removed outlier: 3.714A 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 99 removed outlier: 4.058A 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: 3.577A pdb=" N TYR A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 131 Processing helix chain 'A' and resid 133 through 146 removed outlier: 4.239A 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 192 Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 220 through 238 Processing helix chain 'A' and resid 239 through 244 removed outlier: 5.878A pdb=" N ILE A 242 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE A 243 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 259 removed outlier: 3.837A pdb=" N LEU A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 296 Proline residue: A 277 - end of helix removed outlier: 3.780A pdb=" N GLY A 296 " --> pdb=" O TRP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 313 removed outlier: 3.512A pdb=" N GLN A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 327 Processing helix chain 'A' and resid 333 through 353 removed outlier: 3.521A pdb=" N ARG A 353 " --> pdb=" O MET A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 386 removed outlier: 3.977A pdb=" N THR A 376 " --> pdb=" O ASN A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 397 removed outlier: 4.264A pdb=" N CYS A 396 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 421 Processing helix chain 'A' and resid 423 through 443 removed outlier: 4.371A pdb=" N PHE A 427 " --> pdb=" O TRP A 423 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 452 removed outlier: 3.500A pdb=" N LEU A 447 " --> pdb=" O GLY A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 457 removed outlier: 4.093A pdb=" N VAL A 457 " --> pdb=" O GLY A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 477 removed outlier: 4.248A pdb=" N PHE A 477 " --> pdb=" O PHE A 473 " (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: 3.927A 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 519 through 522 Processing helix chain 'A' and resid 523 through 534 Processing helix chain 'A' and resid 536 through 544 Processing helix chain 'A' and resid 544 through 567 removed outlier: 3.558A pdb=" N THR A 548 " --> pdb=" O GLY A 544 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLY A 563 " --> pdb=" O CYS A 559 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LEU A 564 " --> pdb=" O GLN A 560 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 584 Processing helix chain 'B' and resid 33 through 53 removed outlier: 3.914A pdb=" N PHE B 37 " --> pdb=" O CYS B 33 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA B 38 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LYS B 42 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLY B 43 " --> pdb=" O ASN B 39 " (cutoff:3.500A) Proline residue: B 50 - end of helix Processing helix chain 'B' and resid 53 through 60 removed outlier: 4.161A pdb=" N MET B 57 " --> pdb=" O CYS B 53 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 81 removed outlier: 3.629A pdb=" N ARG B 66 " --> pdb=" O GLY B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 90 removed outlier: 3.564A pdb=" N MET B 90 " --> pdb=" O TYR B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 removed outlier: 4.102A 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 111 removed outlier: 3.628A pdb=" N TYR B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 131 Processing helix chain 'B' and resid 133 through 146 removed outlier: 4.123A 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 192 Proline residue: B 179 - end of helix Processing helix chain 'B' and resid 220 through 238 Processing helix chain 'B' and resid 239 through 244 removed outlier: 5.841A pdb=" N ILE B 242 " --> pdb=" O CYS B 239 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE B 243 " --> pdb=" O GLY B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 259 removed outlier: 3.855A 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 Processing helix chain 'B' and resid 302 through 314 Processing helix chain 'B' and resid 315 through 328 Processing helix chain 'B' and resid 333 through 352 Processing helix chain 'B' and resid 373 through 386 removed outlier: 3.730A pdb=" N ILE B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 384 " --> pdb=" O VAL B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 395 removed outlier: 3.534A pdb=" N ARG B 394 " --> pdb=" O ALA B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 421 Processing helix chain 'B' and resid 423 through 443 removed outlier: 4.365A pdb=" N PHE B 427 " --> pdb=" O TRP B 423 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY B 443 " --> pdb=" O SER B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 452 removed outlier: 3.554A pdb=" N LEU B 447 " --> pdb=" O GLY B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 458 removed outlier: 3.929A pdb=" N VAL B 457 " --> pdb=" O GLY B 454 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 458 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 476 removed outlier: 3.508A pdb=" N LEU B 463 " --> pdb=" O PRO B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 498 Proline residue: B 489 - end of helix Processing helix chain 'B' and resid 501 through 513 removed outlier: 4.034A 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 534 Processing helix chain 'B' and resid 536 through 567 removed outlier: 4.980A pdb=" N GLY B 546 " --> pdb=" O ILE B 542 " (cutoff:3.500A) Proline residue: B 547 - end of helix removed outlier: 4.016A pdb=" N GLY B 563 " --> pdb=" O CYS B 559 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N LEU B 564 " --> pdb=" O GLN B 560 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL B 565 " --> pdb=" O THR B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 584 552 hydrogen bonds defined for protein. 1638 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: 2.20 Time building geometry restraints manager: 2.48 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: 1302 1.32 - 1.44: 2288 1.44 - 1.57: 4992 1.57 - 1.69: 4 1.69 - 1.81: 144 Bond restraints: 8730 Sorted by residual: bond pdb=" N ILE A 370 " pdb=" CA ILE A 370 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.17e-02 7.31e+03 8.89e+00 bond pdb=" N ILE A 145 " pdb=" CA ILE A 145 " ideal model delta sigma weight residual 1.461 1.495 -0.035 1.19e-02 7.06e+03 8.43e+00 bond pdb=" N ASN A 366 " pdb=" CA ASN A 366 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.26e-02 6.30e+03 8.23e+00 bond pdb=" N MET B 295 " pdb=" CA MET B 295 " ideal model delta sigma weight residual 1.456 1.491 -0.034 1.22e-02 6.72e+03 7.87e+00 bond pdb=" N ILE A 357 " pdb=" CA ILE A 357 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.83e+00 ... (remaining 8725 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 11523 2.10 - 4.19: 298 4.19 - 6.28: 37 6.28 - 8.38: 2 8.38 - 10.47: 2 Bond angle restraints: 11862 Sorted by residual: angle pdb=" CA VAL A 146 " pdb=" C VAL A 146 " pdb=" O VAL A 146 " ideal model delta sigma weight residual 122.13 117.95 4.18 1.11e+00 8.12e-01 1.42e+01 angle pdb=" C ARG A 353 " pdb=" N LYS A 354 " pdb=" CA LYS A 354 " ideal model delta sigma weight residual 122.37 118.95 3.42 9.30e-01 1.16e+00 1.35e+01 angle pdb=" CA LEU A 365 " pdb=" C LEU A 365 " pdb=" O LEU A 365 " ideal model delta sigma weight residual 122.63 117.99 4.64 1.29e+00 6.01e-01 1.29e+01 angle pdb=" N GLY A 356 " pdb=" CA GLY A 356 " pdb=" C GLY A 356 " ideal model delta sigma weight residual 114.66 110.24 4.42 1.24e+00 6.50e-01 1.27e+01 angle pdb=" O11 PTY B 601 " pdb=" P1 PTY B 601 " pdb=" O14 PTY B 601 " ideal model delta sigma weight residual 92.90 103.37 -10.47 3.00e+00 1.11e-01 1.22e+01 ... (remaining 11857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.04: 5033 24.04 - 48.08: 157 48.08 - 72.13: 12 72.13 - 96.17: 1 96.17 - 120.21: 3 Dihedral angle restraints: 5206 sinusoidal: 2082 harmonic: 3124 Sorted by residual: dihedral pdb=" C3 PTY B 601 " pdb=" O11 PTY B 601 " pdb=" P1 PTY B 601 " pdb=" O12 PTY B 601 " ideal model delta sinusoidal sigma weight residual -59.77 -179.98 120.21 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C3 PTY A 601 " pdb=" O11 PTY A 601 " pdb=" P1 PTY A 601 " pdb=" O12 PTY A 601 " ideal model delta sinusoidal sigma weight residual -59.77 -179.52 119.75 1 3.00e+01 1.11e-03 1.60e+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 -179.17 -115.50 1 3.00e+01 1.11e-03 1.53e+01 ... (remaining 5203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 992 0.045 - 0.090: 284 0.090 - 0.135: 81 0.135 - 0.179: 20 0.179 - 0.224: 7 Chirality restraints: 1384 Sorted by residual: chirality pdb=" CA ILE A 370 " pdb=" N ILE A 370 " pdb=" C ILE A 370 " pdb=" CB ILE A 370 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.26e+00 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 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ILE A 357 " pdb=" N ILE A 357 " pdb=" C ILE A 357 " pdb=" CB ILE A 357 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.88e-01 ... (remaining 1381 not shown) Planarity restraints: 1442 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 523 " 0.026 5.00e-02 4.00e+02 3.87e-02 2.39e+00 pdb=" N PRO B 524 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 524 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 524 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 523 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.34e+00 pdb=" N PRO A 524 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 524 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 524 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 361 " 0.017 2.00e-02 2.50e+03 9.59e-03 2.30e+00 pdb=" CG TRP A 361 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP A 361 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP A 361 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP A 361 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 361 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 361 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 361 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 361 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 361 " 0.008 2.00e-02 2.50e+03 ... (remaining 1439 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 960 2.74 - 3.28: 8735 3.28 - 3.82: 13496 3.82 - 4.36: 15580 4.36 - 4.90: 27546 Nonbonded interactions: 66317 Sorted by model distance: nonbonded pdb=" OH TYR B 350 " pdb=" OG1 THR B 376 " model vdw 2.204 3.040 nonbonded pdb=" OD1 ASP A 105 " pdb=" N GLN A 106 " model vdw 2.303 3.120 nonbonded pdb=" OD1 ASP A 316 " pdb=" N VAL A 317 " model vdw 2.319 3.120 nonbonded pdb=" O GLU A 187 " pdb=" NE2 GLN A 191 " model vdw 2.350 3.120 nonbonded pdb=" ND2 ASN B 261 " pdb=" O7 NAG B 602 " model vdw 2.363 3.120 ... (remaining 66312 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 0.350 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 21.350 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 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 : 0.006 0.043 8730 Z= 0.393 Angle : 0.739 10.475 11862 Z= 0.462 Chirality : 0.048 0.224 1384 Planarity : 0.005 0.039 1442 Dihedral : 11.803 120.211 3194 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.33 % Allowed : 0.33 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.25), residues: 1070 helix: 2.13 (0.18), residues: 780 sheet: None (None), residues: 0 loop : -0.87 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 361 HIS 0.008 0.001 HIS B 335 PHE 0.022 0.001 PHE B 251 TYR 0.020 0.002 TYR A 111 ARG 0.004 0.000 ARG B 371 *********************** 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 91 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 1.218 Fit side-chains REVERT: A 295 MET cc_start: 0.8576 (mmt) cc_final: 0.8299 (mmm) outliers start: 3 outliers final: 0 residues processed: 90 average time/residue: 1.3003 time to fit residues: 125.6837 Evaluate side-chains 78 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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: 5.9990 chunk 80 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 0.2980 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 480 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.072886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.053407 restraints weight = 21660.690| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 3.19 r_work: 0.2558 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8730 Z= 0.183 Angle : 0.556 7.662 11862 Z= 0.301 Chirality : 0.040 0.168 1384 Planarity : 0.005 0.044 1442 Dihedral : 7.231 81.201 1272 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.44 % Allowed : 6.07 % Favored : 93.49 % 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: 2.21 (0.18), residues: 782 sheet: None (None), residues: 0 loop : -0.73 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 292 HIS 0.004 0.001 HIS A 335 PHE 0.035 0.001 PHE A 251 TYR 0.036 0.002 TYR B 282 ARG 0.002 0.000 ARG A 353 *********************** 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 86 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.894 Fit side-chains REVERT: B 369 ASP cc_start: 0.8179 (m-30) cc_final: 0.7893 (t0) outliers start: 4 outliers final: 1 residues processed: 82 average time/residue: 1.5453 time to fit residues: 135.5879 Evaluate side-chains 76 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 79 optimal weight: 8.9990 chunk 105 optimal weight: 8.9990 chunk 34 optimal weight: 0.2980 chunk 93 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.071595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.052272 restraints weight = 22146.781| |-----------------------------------------------------------------------------| r_work (start): 0.2664 rms_B_bonded: 3.19 r_work: 0.2527 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8730 Z= 0.236 Angle : 0.543 7.202 11862 Z= 0.289 Chirality : 0.040 0.168 1384 Planarity : 0.005 0.053 1442 Dihedral : 6.616 62.125 1272 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.44 % Allowed : 9.27 % Favored : 90.29 % 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: 2.29 (0.18), residues: 780 sheet: None (None), residues: 0 loop : -0.69 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 414 HIS 0.006 0.001 HIS B 335 PHE 0.029 0.001 PHE A 251 TYR 0.030 0.002 TYR B 282 ARG 0.002 0.000 ARG A 353 *********************** 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 80 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 1.175 Fit side-chains REVERT: B 369 ASP cc_start: 0.8137 (m-30) cc_final: 0.7838 (t0) outliers start: 4 outliers final: 3 residues processed: 78 average time/residue: 1.7298 time to fit residues: 143.2483 Evaluate side-chains 78 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain B residue 118 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 54 optimal weight: 0.0040 chunk 24 optimal weight: 5.9990 chunk 72 optimal weight: 0.4980 chunk 70 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 overall best weight: 3.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.069593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.050404 restraints weight = 22225.343| |-----------------------------------------------------------------------------| r_work (start): 0.2618 rms_B_bonded: 3.15 r_work: 0.2477 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8730 Z= 0.340 Angle : 0.576 7.295 11862 Z= 0.308 Chirality : 0.042 0.180 1384 Planarity : 0.005 0.051 1442 Dihedral : 6.716 58.431 1272 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.88 % Allowed : 10.93 % Favored : 88.19 % 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: 2.22 (0.26), residues: 1070 helix: 2.26 (0.18), residues: 778 sheet: None (None), residues: 0 loop : -0.75 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 414 HIS 0.008 0.001 HIS B 335 PHE 0.028 0.001 PHE A 251 TYR 0.027 0.002 TYR B 282 ARG 0.001 0.000 ARG A 353 *********************** 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 : 1.015 Fit side-chains REVERT: A 114 ASP cc_start: 0.8601 (p0) cc_final: 0.8389 (p0) REVERT: B 369 ASP cc_start: 0.8058 (m-30) cc_final: 0.7741 (t0) outliers start: 8 outliers final: 2 residues processed: 80 average time/residue: 1.3247 time to fit residues: 113.2026 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 : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 266 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 32 optimal weight: 0.1980 chunk 77 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 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 = 0.072860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.053439 restraints weight = 21760.127| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 3.18 r_work: 0.2557 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8730 Z= 0.168 Angle : 0.509 7.186 11862 Z= 0.271 Chirality : 0.039 0.161 1384 Planarity : 0.005 0.066 1442 Dihedral : 6.413 55.715 1272 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.88 % Allowed : 11.92 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.26 (0.26), residues: 1070 helix: 2.26 (0.18), residues: 780 sheet: None (None), residues: 0 loop : -0.66 (0.39), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 414 HIS 0.003 0.001 HIS B 335 PHE 0.025 0.001 PHE A 251 TYR 0.027 0.001 TYR B 282 ARG 0.002 0.000 ARG B 371 *********************** 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 86 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.955 Fit side-chains REVERT: A 114 ASP cc_start: 0.8382 (p0) cc_final: 0.8110 (p0) REVERT: B 369 ASP cc_start: 0.7983 (m-30) cc_final: 0.7652 (t0) outliers start: 8 outliers final: 1 residues processed: 81 average time/residue: 1.2374 time to fit residues: 107.2677 Evaluate side-chains 76 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.072034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.052653 restraints weight = 21794.309| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 3.18 r_work: 0.2537 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8730 Z= 0.206 Angle : 0.521 7.078 11862 Z= 0.274 Chirality : 0.039 0.166 1384 Planarity : 0.005 0.063 1442 Dihedral : 6.382 58.245 1272 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.77 % Allowed : 13.25 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.26), residues: 1070 helix: 2.35 (0.18), residues: 778 sheet: None (None), residues: 0 loop : -0.77 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 414 HIS 0.005 0.001 HIS B 335 PHE 0.024 0.001 PHE A 251 TYR 0.025 0.001 TYR B 282 ARG 0.001 0.000 ARG A 353 *********************** 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 81 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 1.149 Fit side-chains REVERT: A 562 TRP cc_start: 0.8243 (OUTLIER) cc_final: 0.8032 (t60) REVERT: B 369 ASP cc_start: 0.7929 (m-30) cc_final: 0.7571 (t0) outliers start: 7 outliers final: 3 residues processed: 79 average time/residue: 1.3369 time to fit residues: 112.6370 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 : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 562 TRP Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 463 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 49 optimal weight: 10.0000 chunk 81 optimal weight: 0.0970 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 0.0770 chunk 79 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.074544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.055213 restraints weight = 21573.240| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 3.20 r_work: 0.2596 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8730 Z= 0.154 Angle : 0.496 7.024 11862 Z= 0.260 Chirality : 0.038 0.156 1384 Planarity : 0.005 0.065 1442 Dihedral : 6.217 56.656 1272 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.99 % Allowed : 13.58 % Favored : 85.43 % 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: 2.32 (0.26), residues: 1070 helix: 2.32 (0.18), residues: 778 sheet: None (None), residues: 0 loop : -0.66 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 414 HIS 0.003 0.001 HIS A 335 PHE 0.022 0.001 PHE A 251 TYR 0.025 0.001 TYR B 282 ARG 0.001 0.000 ARG B 371 *********************** 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 89 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.967 Fit side-chains REVERT: A 372 ASN cc_start: 0.8441 (m110) cc_final: 0.8096 (m-40) REVERT: B 326 TYR cc_start: 0.8846 (OUTLIER) cc_final: 0.8390 (m-80) REVERT: B 369 ASP cc_start: 0.7904 (m-30) cc_final: 0.7540 (t0) outliers start: 9 outliers final: 3 residues processed: 85 average time/residue: 1.2850 time to fit residues: 116.9234 Evaluate side-chains 82 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain B residue 326 TYR Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 570 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 18 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 23 optimal weight: 0.4980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.074091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.054666 restraints weight = 22052.955| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 3.23 r_work: 0.2580 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8730 Z= 0.168 Angle : 0.504 7.008 11862 Z= 0.262 Chirality : 0.038 0.158 1384 Planarity : 0.004 0.064 1442 Dihedral : 6.198 58.443 1272 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.21 % Allowed : 13.69 % Favored : 85.10 % 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: 2.24 (0.26), residues: 1070 helix: 2.25 (0.18), residues: 792 sheet: None (None), residues: 0 loop : -0.82 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 414 HIS 0.004 0.001 HIS B 335 PHE 0.021 0.001 PHE A 251 TYR 0.024 0.001 TYR B 282 ARG 0.001 0.000 ARG B 325 *********************** 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 89 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.890 Fit side-chains REVERT: B 326 TYR cc_start: 0.8834 (OUTLIER) cc_final: 0.8383 (m-80) REVERT: B 369 ASP cc_start: 0.7866 (m-30) cc_final: 0.7498 (t0) outliers start: 11 outliers final: 3 residues processed: 87 average time/residue: 1.2436 time to fit residues: 115.7662 Evaluate side-chains 80 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain B residue 326 TYR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 463 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 37 optimal weight: 0.0970 chunk 99 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 44 optimal weight: 0.0770 chunk 11 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 372 ASN ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.076638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.057199 restraints weight = 21708.994| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 3.22 r_work: 0.2649 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8730 Z= 0.139 Angle : 0.492 7.072 11862 Z= 0.254 Chirality : 0.038 0.150 1384 Planarity : 0.004 0.064 1442 Dihedral : 6.052 57.880 1272 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.55 % Allowed : 14.57 % Favored : 84.88 % 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: 2.25 (0.26), residues: 1070 helix: 2.24 (0.18), residues: 792 sheet: None (None), residues: 0 loop : -0.77 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 414 HIS 0.003 0.001 HIS A 135 PHE 0.017 0.001 PHE A 251 TYR 0.024 0.001 TYR B 282 ARG 0.001 0.000 ARG A 353 *********************** 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 86 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.958 Fit side-chains REVERT: B 316 ASP cc_start: 0.8897 (p0) cc_final: 0.8401 (m-30) REVERT: B 369 ASP cc_start: 0.7797 (m-30) cc_final: 0.7414 (t0) outliers start: 5 outliers final: 1 residues processed: 85 average time/residue: 1.1738 time to fit residues: 106.9997 Evaluate side-chains 78 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 18 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 25 optimal weight: 0.3980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.076232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.056377 restraints weight = 20954.915| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 3.16 r_work: 0.2614 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8730 Z= 0.164 Angle : 0.507 7.804 11862 Z= 0.259 Chirality : 0.038 0.156 1384 Planarity : 0.004 0.063 1442 Dihedral : 6.069 59.143 1272 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.22 % Allowed : 15.23 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.26), residues: 1070 helix: 2.30 (0.18), residues: 790 sheet: None (None), residues: 0 loop : -0.76 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 414 HIS 0.003 0.001 HIS A 335 PHE 0.019 0.001 PHE A 251 TYR 0.024 0.001 TYR B 282 ARG 0.001 0.000 ARG B 325 ********************** 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: 2 poor density : 77 time to evaluate : 0.883 Fit side-chains REVERT: B 316 ASP cc_start: 0.8871 (p0) cc_final: 0.8392 (m-30) REVERT: B 369 ASP cc_start: 0.7818 (m-30) cc_final: 0.7438 (t0) outliers start: 2 outliers final: 2 residues processed: 78 average time/residue: 1.2706 time to fit residues: 105.7648 Evaluate side-chains 79 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 359 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 70 optimal weight: 0.1980 chunk 75 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 6 optimal weight: 0.0980 chunk 12 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 27 optimal weight: 0.2980 chunk 55 optimal weight: 0.0770 overall best weight: 0.3340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.077941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.057976 restraints weight = 20900.936| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 3.16 r_work: 0.2661 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8730 Z= 0.137 Angle : 0.493 7.469 11862 Z= 0.252 Chirality : 0.037 0.148 1384 Planarity : 0.004 0.064 1442 Dihedral : 5.983 58.174 1272 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.33 % Allowed : 14.90 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.26), residues: 1070 helix: 2.38 (0.18), residues: 778 sheet: None (None), residues: 0 loop : -0.81 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 414 HIS 0.003 0.001 HIS A 135 PHE 0.016 0.001 PHE A 251 TYR 0.025 0.001 TYR B 282 ARG 0.001 0.000 ARG B 536 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5233.91 seconds wall clock time: 92 minutes 23.95 seconds (5543.95 seconds total)