Starting phenix.real_space_refine on Fri Dec 8 10:23:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fti_29433/12_2023/8fti_29433.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fti_29433/12_2023/8fti_29433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fti_29433/12_2023/8fti_29433.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fti_29433/12_2023/8fti_29433.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fti_29433/12_2023/8fti_29433.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fti_29433/12_2023/8fti_29433.pdb" } resolution = 3.5 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= 0.000 sd= 0.020 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 97 5.49 5 S 24 5.16 5 C 4792 2.51 5 N 1443 2.21 5 O 1770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8126 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 6062 Classifications: {'peptide': 737} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 725} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 2064 Classifications: {'RNA': 97} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 9, 'rna3p_pur': 45, 'rna3p_pyr': 38} Link IDs: {'rna2p': 13, 'rna3p': 83} Chain breaks: 1 Time building chain proxies: 4.59, per 1000 atoms: 0.56 Number of scatterers: 8126 At special positions: 0 Unit cell: (77.43, 81.78, 137.46, 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 24 16.00 P 97 15.00 O 1770 8.00 N 1443 7.00 C 4792 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.50 Conformation dependent library (CDL) restraints added in 1.2 seconds 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1380 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 3 sheets defined 61.9% alpha, 3.7% beta 33 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 2.68 Creating SS restraints... Processing helix chain 'A' and resid 20 through 24 removed outlier: 3.639A pdb=" N ARG A 23 " --> pdb=" O GLN A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 41 removed outlier: 3.980A pdb=" N ILE A 29 " --> pdb=" O TRP A 25 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A 30 " --> pdb=" O CYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 50 Processing helix chain 'A' and resid 62 through 72 Processing helix chain 'A' and resid 75 through 89 removed outlier: 3.641A pdb=" N LYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 123 removed outlier: 3.509A pdb=" N THR A 107 " --> pdb=" O ASP A 103 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 151 removed outlier: 4.133A pdb=" N PHE A 151 " --> pdb=" O PHE A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 Processing helix chain 'A' and resid 166 through 170 removed outlier: 3.676A pdb=" N LYS A 170 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 184 Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.616A pdb=" N ASP A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 221 removed outlier: 3.751A pdb=" N TYR A 220 " --> pdb=" O GLU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 258 removed outlier: 3.707A pdb=" N PHE A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 338 removed outlier: 3.624A pdb=" N TYR A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 360 removed outlier: 3.652A pdb=" N ALA A 343 " --> pdb=" O LYS A 339 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARG A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLN A 352 " --> pdb=" O TYR A 348 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 373 through 380 removed outlier: 3.741A pdb=" N LEU A 377 " --> pdb=" O PRO A 373 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N HIS A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 408 Processing helix chain 'A' and resid 413 through 429 removed outlier: 3.777A pdb=" N TYR A 424 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 425 " --> pdb=" O ILE A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 447 removed outlier: 3.992A pdb=" N ASN A 439 " --> pdb=" O PRO A 435 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 463 removed outlier: 3.624A pdb=" N PHE A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 476 removed outlier: 3.844A pdb=" N TYR A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLN A 476 " --> pdb=" O SER A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 497 Processing helix chain 'A' and resid 500 through 508 Processing helix chain 'A' and resid 516 through 527 removed outlier: 3.691A pdb=" N LYS A 520 " --> pdb=" O ASP A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 540 removed outlier: 3.723A pdb=" N LYS A 537 " --> pdb=" O GLY A 533 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 558 removed outlier: 3.592A pdb=" N HIS A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 606 removed outlier: 3.758A pdb=" N LEU A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU A 588 " --> pdb=" O PRO A 584 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A 591 " --> pdb=" O TYR A 587 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU A 595 " --> pdb=" O ALA A 591 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 604 " --> pdb=" O ALA A 600 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 606 " --> pdb=" O TYR A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 644 Processing helix chain 'A' and resid 652 through 662 removed outlier: 3.628A pdb=" N GLY A 656 " --> pdb=" O ALA A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 706 removed outlier: 3.970A pdb=" N PHE A 680 " --> pdb=" O TYR A 676 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ARG A 681 " --> pdb=" O GLU A 677 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A 682 " --> pdb=" O LYS A 678 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS A 689 " --> pdb=" O ASP A 685 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS A 706 " --> pdb=" O VAL A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 725 Processing helix chain 'A' and resid 728 through 744 Processing helix chain 'A' and resid 750 through 764 removed outlier: 4.374A pdb=" N PHE A 754 " --> pdb=" O VAL A 750 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY A 755 " --> pdb=" O ILE A 751 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR A 764 " --> pdb=" O VAL A 760 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 289 through 291 removed outlier: 3.831A pdb=" N VAL A 289 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS A 267 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER A 300 " --> pdb=" O ARG A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 307 through 314 removed outlier: 4.226A pdb=" N LYS A 314 " --> pdb=" O GLY A 317 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A 317 " --> pdb=" O LYS A 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 616 through 618 290 hydrogen bonds defined for protein. 852 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 3.03 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1843 1.33 - 1.45: 2318 1.45 - 1.57: 4105 1.57 - 1.69: 192 1.69 - 1.81: 34 Bond restraints: 8492 Sorted by residual: bond pdb=" C TRP A 770 " pdb=" N LYS A 771 " ideal model delta sigma weight residual 1.328 1.339 -0.011 1.30e-02 5.92e+03 6.93e-01 bond pdb=" CA GLN A 74 " pdb=" CB GLN A 74 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 6.55e-01 bond pdb=" N LYS A 771 " pdb=" CA LYS A 771 " ideal model delta sigma weight residual 1.460 1.471 -0.011 1.42e-02 4.96e+03 6.01e-01 bond pdb=" C LEU A 649 " pdb=" N ASP A 650 " ideal model delta sigma weight residual 1.327 1.334 -0.007 9.40e-03 1.13e+04 5.85e-01 bond pdb=" N ASN A 238 " pdb=" CA ASN A 238 " ideal model delta sigma weight residual 1.463 1.456 0.008 1.08e-02 8.57e+03 5.11e-01 ... (remaining 8487 not shown) Histogram of bond angle deviations from ideal: 100.40 - 107.12: 639 107.12 - 113.84: 4855 113.84 - 120.55: 3510 120.55 - 127.27: 2645 127.27 - 133.99: 236 Bond angle restraints: 11885 Sorted by residual: angle pdb=" C THR A 73 " pdb=" N GLN A 74 " pdb=" CA GLN A 74 " ideal model delta sigma weight residual 121.54 128.41 -6.87 1.91e+00 2.74e-01 1.29e+01 angle pdb=" C ALA A 463 " pdb=" N GLU A 464 " pdb=" CA GLU A 464 " ideal model delta sigma weight residual 122.74 126.45 -3.71 1.44e+00 4.82e-01 6.65e+00 angle pdb=" N ASN A 583 " pdb=" CA ASN A 583 " pdb=" C ASN A 583 " ideal model delta sigma weight residual 109.81 114.81 -5.00 2.21e+00 2.05e-01 5.11e+00 angle pdb=" CA ASN A 583 " pdb=" C ASN A 583 " pdb=" N PRO A 584 " ideal model delta sigma weight residual 118.44 121.89 -3.45 1.59e+00 3.96e-01 4.72e+00 angle pdb=" C PRO A 773 " pdb=" N VAL A 774 " pdb=" CA VAL A 774 " ideal model delta sigma weight residual 121.97 125.86 -3.89 1.80e+00 3.09e-01 4.66e+00 ... (remaining 11880 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.54: 4834 34.54 - 69.07: 238 69.07 - 103.61: 24 103.61 - 138.15: 0 138.15 - 172.68: 1 Dihedral angle restraints: 5097 sinusoidal: 2947 harmonic: 2150 Sorted by residual: dihedral pdb=" CA GLY A 644 " pdb=" C GLY A 644 " pdb=" N LYS A 645 " pdb=" CA LYS A 645 " ideal model delta harmonic sigma weight residual -180.00 -160.23 -19.77 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" C4' C B -1 " pdb=" C3' C B -1 " pdb=" O3' C B -1 " pdb=" P G B 0 " ideal model delta sinusoidal sigma weight residual -140.00 32.68 -172.68 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA ARG A 349 " pdb=" C ARG A 349 " pdb=" N TYR A 350 " pdb=" CA TYR A 350 " ideal model delta harmonic sigma weight residual -180.00 -161.97 -18.03 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 5094 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 979 0.028 - 0.056: 264 0.056 - 0.083: 66 0.083 - 0.111: 34 0.111 - 0.139: 11 Chirality restraints: 1354 Sorted by residual: chirality pdb=" C1' A B -24 " pdb=" O4' A B -24 " pdb=" C2' A B -24 " pdb=" N9 A B -24 " both_signs ideal model delta sigma weight residual False 2.46 2.32 0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA ILE A 213 " pdb=" N ILE A 213 " pdb=" C ILE A 213 " pdb=" CB ILE A 213 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA ILE A 636 " pdb=" N ILE A 636 " pdb=" C ILE A 636 " pdb=" CB ILE A 636 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 1351 not shown) Planarity restraints: 1162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 583 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO A 584 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 584 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 584 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G B 4 " 0.018 2.00e-02 2.50e+03 9.03e-03 2.44e+00 pdb=" N9 G B 4 " -0.025 2.00e-02 2.50e+03 pdb=" C8 G B 4 " -0.000 2.00e-02 2.50e+03 pdb=" N7 G B 4 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G B 4 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G B 4 " 0.002 2.00e-02 2.50e+03 pdb=" O6 G B 4 " 0.002 2.00e-02 2.50e+03 pdb=" N1 G B 4 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G B 4 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G B 4 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G B 4 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G B 4 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B -24 " -0.019 2.00e-02 2.50e+03 8.87e-03 2.16e+00 pdb=" N9 A B -24 " 0.022 2.00e-02 2.50e+03 pdb=" C8 A B -24 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A B -24 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A B -24 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A B -24 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A B -24 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A B -24 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A B -24 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A B -24 " 0.002 2.00e-02 2.50e+03 pdb=" C4 A B -24 " -0.000 2.00e-02 2.50e+03 ... (remaining 1159 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1653 2.77 - 3.30: 7856 3.30 - 3.83: 13459 3.83 - 4.37: 15275 4.37 - 4.90: 23661 Nonbonded interactions: 61904 Sorted by model distance: nonbonded pdb=" OH TYR A 253 " pdb=" OG SER A 335 " model vdw 2.237 2.440 nonbonded pdb=" OE1 GLN A 257 " pdb=" OH TYR A 602 " model vdw 2.250 2.440 nonbonded pdb=" O GLU A 104 " pdb=" OG1 THR A 107 " model vdw 2.255 2.440 nonbonded pdb=" O PHE A 147 " pdb=" OG SER A 150 " model vdw 2.277 2.440 nonbonded pdb=" OE1 GLU A 552 " pdb=" NE ARG A 594 " model vdw 2.303 2.520 ... (remaining 61899 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.970 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 26.190 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 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 : 0.002 0.026 8492 Z= 0.157 Angle : 0.559 6.869 11885 Z= 0.323 Chirality : 0.032 0.139 1354 Planarity : 0.003 0.047 1162 Dihedral : 17.208 172.685 3717 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.55 % Allowed : 10.34 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.31), residues: 729 helix: 1.10 (0.25), residues: 419 sheet: -0.24 (1.17), residues: 27 loop : -1.24 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 402 HIS 0.003 0.001 HIS A 554 PHE 0.017 0.001 PHE A 638 TYR 0.013 0.001 TYR A 321 ARG 0.002 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 85 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 12 residues processed: 112 average time/residue: 0.2687 time to fit residues: 38.3494 Evaluate side-chains 71 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 59 time to evaluate : 0.683 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1581 time to fit residues: 3.6086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 0.0870 chunk 41 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 47 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 HIS A 476 GLN A 561 GLN ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8492 Z= 0.170 Angle : 0.535 5.587 11885 Z= 0.285 Chirality : 0.035 0.158 1354 Planarity : 0.003 0.046 1162 Dihedral : 18.005 173.626 2204 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.35 % Allowed : 15.83 % Favored : 81.82 % 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: 0.63 (0.31), residues: 729 helix: 1.58 (0.25), residues: 427 sheet: -0.27 (1.18), residues: 27 loop : -1.41 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 770 HIS 0.003 0.001 HIS A 673 PHE 0.021 0.001 PHE A 638 TYR 0.014 0.001 TYR A 321 ARG 0.004 0.000 ARG A 459 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 69 time to evaluate : 0.804 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 80 average time/residue: 0.2253 time to fit residues: 24.4475 Evaluate side-chains 76 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 0.804 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0758 time to fit residues: 2.4394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 25 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 HIS ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8492 Z= 0.152 Angle : 0.500 5.427 11885 Z= 0.264 Chirality : 0.034 0.154 1354 Planarity : 0.003 0.044 1162 Dihedral : 17.917 172.935 2204 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.72 % Allowed : 17.87 % Favored : 80.41 % 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: 0.86 (0.31), residues: 729 helix: 1.88 (0.26), residues: 422 sheet: -0.32 (1.11), residues: 29 loop : -1.47 (0.32), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 60 HIS 0.003 0.001 HIS A 554 PHE 0.021 0.001 PHE A 638 TYR 0.013 0.001 TYR A 321 ARG 0.004 0.000 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.768 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 76 average time/residue: 0.2186 time to fit residues: 22.8013 Evaluate side-chains 60 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.769 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0800 time to fit residues: 1.3214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 21 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8492 Z= 0.169 Angle : 0.525 10.270 11885 Z= 0.273 Chirality : 0.034 0.182 1354 Planarity : 0.003 0.046 1162 Dihedral : 17.896 173.202 2204 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.45 % Allowed : 18.65 % Favored : 77.90 % 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: 0.67 (0.31), residues: 729 helix: 1.72 (0.25), residues: 422 sheet: -0.47 (1.09), residues: 29 loop : -1.53 (0.32), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 60 HIS 0.004 0.001 HIS A 353 PHE 0.023 0.001 PHE A 638 TYR 0.023 0.001 TYR A 175 ARG 0.005 0.000 ARG A 681 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 62 time to evaluate : 0.723 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 79 average time/residue: 0.2235 time to fit residues: 24.1687 Evaluate side-chains 73 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 0.822 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0782 time to fit residues: 2.9415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 54 optimal weight: 0.0570 chunk 0 optimal weight: 20.0000 chunk 40 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 overall best weight: 2.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8492 Z= 0.255 Angle : 0.586 8.538 11885 Z= 0.307 Chirality : 0.037 0.214 1354 Planarity : 0.004 0.050 1162 Dihedral : 18.064 175.331 2204 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.19 % Allowed : 19.91 % Favored : 77.90 % 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: 0.43 (0.31), residues: 729 helix: 1.59 (0.26), residues: 418 sheet: -0.52 (1.03), residues: 31 loop : -1.71 (0.32), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 402 HIS 0.005 0.001 HIS A 415 PHE 0.024 0.002 PHE A 638 TYR 0.019 0.002 TYR A 321 ARG 0.003 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 60 time to evaluate : 0.771 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 73 average time/residue: 0.2278 time to fit residues: 22.9630 Evaluate side-chains 63 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 0.786 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0870 time to fit residues: 2.0997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8492 Z= 0.275 Angle : 0.611 7.780 11885 Z= 0.319 Chirality : 0.038 0.223 1354 Planarity : 0.004 0.053 1162 Dihedral : 18.113 176.450 2204 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.51 % Allowed : 21.47 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.30), residues: 729 helix: 1.35 (0.25), residues: 418 sheet: -0.72 (1.02), residues: 31 loop : -1.80 (0.31), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 402 HIS 0.005 0.001 HIS A 415 PHE 0.025 0.002 PHE A 638 TYR 0.021 0.002 TYR A 175 ARG 0.003 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 57 time to evaluate : 0.699 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 71 average time/residue: 0.2102 time to fit residues: 20.6973 Evaluate side-chains 62 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.802 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0778 time to fit residues: 2.2469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8492 Z= 0.182 Angle : 0.549 7.025 11885 Z= 0.288 Chirality : 0.035 0.213 1354 Planarity : 0.003 0.052 1162 Dihedral : 17.914 174.406 2204 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.41 % Allowed : 21.63 % Favored : 76.96 % 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: 0.38 (0.31), residues: 729 helix: 1.56 (0.25), residues: 418 sheet: -0.57 (1.03), residues: 31 loop : -1.74 (0.32), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 60 HIS 0.003 0.001 HIS A 554 PHE 0.023 0.001 PHE A 638 TYR 0.021 0.001 TYR A 471 ARG 0.003 0.000 ARG A 681 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 66 average time/residue: 0.2258 time to fit residues: 20.5298 Evaluate side-chains 59 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.689 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0698 time to fit residues: 1.4527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8492 Z= 0.252 Angle : 0.604 8.866 11885 Z= 0.314 Chirality : 0.037 0.249 1354 Planarity : 0.004 0.051 1162 Dihedral : 17.982 175.730 2204 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.94 % Allowed : 23.04 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.31), residues: 729 helix: 1.43 (0.25), residues: 418 sheet: -0.74 (1.01), residues: 31 loop : -1.83 (0.32), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 60 HIS 0.004 0.001 HIS A 415 PHE 0.025 0.002 PHE A 638 TYR 0.024 0.002 TYR A 175 ARG 0.003 0.000 ARG A 657 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.751 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 61 average time/residue: 0.2234 time to fit residues: 18.9120 Evaluate side-chains 57 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 0.679 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0739 time to fit residues: 1.1897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 69 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8492 Z= 0.233 Angle : 0.590 8.740 11885 Z= 0.309 Chirality : 0.037 0.248 1354 Planarity : 0.004 0.051 1162 Dihedral : 17.953 175.482 2204 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.31 % Allowed : 23.51 % Favored : 76.18 % 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: 0.21 (0.31), residues: 729 helix: 1.43 (0.25), residues: 418 sheet: -0.73 (1.02), residues: 31 loop : -1.84 (0.33), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 60 HIS 0.004 0.001 HIS A 415 PHE 0.023 0.002 PHE A 638 TYR 0.016 0.001 TYR A 321 ARG 0.003 0.000 ARG A 681 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.776 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 61 average time/residue: 0.2185 time to fit residues: 18.5150 Evaluate side-chains 59 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.776 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0753 time to fit residues: 1.2891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8492 Z= 0.199 Angle : 0.571 8.727 11885 Z= 0.300 Chirality : 0.036 0.290 1354 Planarity : 0.004 0.051 1162 Dihedral : 17.875 174.597 2204 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.47 % Allowed : 23.51 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.31), residues: 729 helix: 1.46 (0.25), residues: 418 sheet: -0.63 (1.02), residues: 31 loop : -1.82 (0.33), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 60 HIS 0.003 0.001 HIS A 415 PHE 0.024 0.002 PHE A 638 TYR 0.026 0.001 TYR A 175 ARG 0.003 0.000 ARG A 681 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.726 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 59 average time/residue: 0.2344 time to fit residues: 18.6760 Evaluate side-chains 54 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.709 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0710 time to fit residues: 1.0736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 57 optimal weight: 0.4980 chunk 3 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 687 GLN ** 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 = 0.4291 r_free = 0.4291 target = 0.160570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.120874 restraints weight = 15382.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.124588 restraints weight = 8694.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.126894 restraints weight = 6230.413| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8492 Z= 0.146 Angle : 0.526 8.929 11885 Z= 0.274 Chirality : 0.034 0.239 1354 Planarity : 0.003 0.049 1162 Dihedral : 17.697 172.319 2204 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.16 % Allowed : 24.14 % Favored : 75.71 % 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: 0.60 (0.31), residues: 729 helix: 1.75 (0.26), residues: 421 sheet: -0.41 (1.10), residues: 29 loop : -1.72 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 60 HIS 0.002 0.001 HIS A 415 PHE 0.019 0.001 PHE A 638 TYR 0.010 0.001 TYR A 321 ARG 0.004 0.000 ARG A 459 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1504.14 seconds wall clock time: 28 minutes 20.49 seconds (1700.49 seconds total)