Starting phenix.real_space_refine (version: dev) on Fri May 13 01:42:48 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a7c_11677/05_2022/7a7c_11677_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a7c_11677/05_2022/7a7c_11677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a7c_11677/05_2022/7a7c_11677.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a7c_11677/05_2022/7a7c_11677.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a7c_11677/05_2022/7a7c_11677_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a7c_11677/05_2022/7a7c_11677_updated.pdb" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.012 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 9387 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4277 Classifications: {'peptide': 560} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 30, 'TRANS': 529} Chain breaks: 4 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'TRP:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 5110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5110 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1, 'peptide': 666} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 43, 'TRANS': 622, None: 1} Not linked: pdbres="VAL B 739 " pdbres="HEM B 801 " Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 6.07, per 1000 atoms: 0.65 Number of scatterers: 9387 At special positions: 0 Unit cell: (84.76, 96.496, 126.488, 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) Fe 1 26.01 S 32 16.00 O 1759 8.00 N 1622 7.00 C 5973 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.97 Conformation dependent library (CDL) restraints added in 1.6 seconds 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2214 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 66 helices and 3 sheets defined 46.6% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 64 through 70 removed outlier: 3.995A pdb=" N THR A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 84 Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 99 through 109 Processing helix chain 'A' and resid 149 through 158 removed outlier: 4.254A pdb=" N LYS A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LYS A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LYS A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 176 removed outlier: 3.574A pdb=" N VAL A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 removed outlier: 3.830A pdb=" N MET A 255 " --> pdb=" O THR A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 269 Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 388 through 398 removed outlier: 3.520A pdb=" N ILE A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 416 Processing helix chain 'A' and resid 423 through 425 No H-bonds generated for 'chain 'A' and resid 423 through 425' Processing helix chain 'A' and resid 437 through 439 No H-bonds generated for 'chain 'A' and resid 437 through 439' Processing helix chain 'A' and resid 453 through 461 Processing helix chain 'A' and resid 469 through 480 removed outlier: 3.581A pdb=" N ALA A 480 " --> pdb=" O ALA A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 500 through 503 No H-bonds generated for 'chain 'A' and resid 500 through 503' Processing helix chain 'A' and resid 514 through 530 Processing helix chain 'A' and resid 540 through 559 removed outlier: 3.719A pdb=" N VAL A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 587 removed outlier: 4.423A pdb=" N VAL A 586 " --> pdb=" O GLU A 582 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LEU A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 616 Processing helix chain 'A' and resid 621 through 633 removed outlier: 3.920A pdb=" N VAL A 633 " --> pdb=" O GLY A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 656 through 661 Processing helix chain 'A' and resid 693 through 700 removed outlier: 4.443A pdb=" N PHE A 698 " --> pdb=" O VAL A 694 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY A 699 " --> pdb=" O ASP A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 711 removed outlier: 3.767A pdb=" N LEU A 707 " --> pdb=" O GLU A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 732 Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 64 through 70 removed outlier: 3.753A pdb=" N THR B 70 " --> pdb=" O ALA B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 85 removed outlier: 3.648A pdb=" N THR B 85 " --> pdb=" O GLU B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 99 through 110 Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 141 through 144 No H-bonds generated for 'chain 'B' and resid 141 through 144' Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 156 through 158 No H-bonds generated for 'chain 'B' and resid 156 through 158' Processing helix chain 'B' and resid 161 through 176 removed outlier: 3.510A pdb=" N VAL B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 removed outlier: 4.024A pdb=" N VAL B 246 " --> pdb=" O MET B 242 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP B 247 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET B 255 " --> pdb=" O THR B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 331 through 336 Processing helix chain 'B' and resid 357 through 359 No H-bonds generated for 'chain 'B' and resid 357 through 359' Processing helix chain 'B' and resid 379 through 386 removed outlier: 4.176A pdb=" N LEU B 384 " --> pdb=" O THR B 380 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ARG B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 399 removed outlier: 3.648A pdb=" N ARG B 392 " --> pdb=" O PRO B 388 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE B 393 " --> pdb=" O ILE B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 416 Processing helix chain 'B' and resid 423 through 425 No H-bonds generated for 'chain 'B' and resid 423 through 425' Processing helix chain 'B' and resid 437 through 439 No H-bonds generated for 'chain 'B' and resid 437 through 439' Processing helix chain 'B' and resid 453 through 465 removed outlier: 3.818A pdb=" N SER B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 480 Processing helix chain 'B' and resid 493 through 498 removed outlier: 4.424A pdb=" N ARG B 496 " --> pdb=" O ASN B 493 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE B 497 " --> pdb=" O GLY B 494 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG B 498 " --> pdb=" O GLY B 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 493 through 498' Processing helix chain 'B' and resid 500 through 503 No H-bonds generated for 'chain 'B' and resid 500 through 503' Processing helix chain 'B' and resid 515 through 530 Processing helix chain 'B' and resid 540 through 559 removed outlier: 3.795A pdb=" N VAL B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 584 No H-bonds generated for 'chain 'B' and resid 582 through 584' Processing helix chain 'B' and resid 606 through 616 Processing helix chain 'B' and resid 621 through 634 removed outlier: 3.905A pdb=" N VAL B 633 " --> pdb=" O GLY B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 640 No H-bonds generated for 'chain 'B' and resid 638 through 640' Processing helix chain 'B' and resid 656 through 661 Processing helix chain 'B' and resid 693 through 700 removed outlier: 4.264A pdb=" N PHE B 698 " --> pdb=" O VAL B 694 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLY B 699 " --> pdb=" O ASP B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 711 removed outlier: 3.815A pdb=" N LEU B 707 " --> pdb=" O GLU B 703 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B 710 " --> pdb=" O ALA B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 732 Processing sheet with id= A, first strand: chain 'A' and resid 667 through 670 removed outlier: 3.538A pdb=" N THR A 667 " --> pdb=" O LYS A 681 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 341 through 344 Processing sheet with id= C, first strand: chain 'B' and resid 667 through 670 305 hydrogen bonds defined for protein. 900 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: 2.54 Time building geometry restraints manager: 4.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.39: 3928 1.39 - 1.56: 5636 1.56 - 1.72: 0 1.72 - 1.89: 60 1.89 - 2.05: 4 Bond restraints: 9628 Sorted by residual: bond pdb=" CA TRP B 39 " pdb=" C TRP B 39 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.10e-02 2.27e+03 7.26e-01 bond pdb=" CA TRP B 351 " pdb=" C TRP B 351 " ideal model delta sigma weight residual 1.523 1.534 -0.011 1.34e-02 5.57e+03 7.06e-01 bond pdb=" CA ILE A 462 " pdb=" C ILE A 462 " ideal model delta sigma weight residual 1.530 1.521 0.009 1.12e-02 7.97e+03 6.65e-01 bond pdb=" CA PRO B 239 " pdb=" C PRO B 239 " ideal model delta sigma weight residual 1.527 1.518 0.009 1.07e-02 8.73e+03 6.49e-01 bond pdb=" CA ASP A 240 " pdb=" C ASP A 240 " ideal model delta sigma weight residual 1.525 1.541 -0.016 2.10e-02 2.27e+03 6.00e-01 ... (remaining 9623 not shown) Histogram of bond angle deviations from ideal: 88.93 - 106.93: 366 106.93 - 124.94: 12492 124.94 - 142.95: 262 142.95 - 160.95: 0 160.95 - 178.96: 2 Bond angle restraints: 13122 Sorted by residual: angle pdb=" N PRO B 642 " pdb=" CA PRO B 642 " pdb=" C PRO B 642 " ideal model delta sigma weight residual 114.68 111.41 3.27 1.04e+00 9.25e-01 9.86e+00 angle pdb=" N ILE A 462 " pdb=" CA ILE A 462 " pdb=" C ILE A 462 " ideal model delta sigma weight residual 111.91 109.66 2.25 8.90e-01 1.26e+00 6.37e+00 angle pdb=" CA TYR B 597 " pdb=" C TYR B 597 " pdb=" N LEU B 598 " ideal model delta sigma weight residual 114.81 118.16 -3.35 1.42e+00 4.96e-01 5.56e+00 angle pdb=" N TYR B 597 " pdb=" CA TYR B 597 " pdb=" C TYR B 597 " ideal model delta sigma weight residual 111.17 113.92 -2.75 1.41e+00 5.03e-01 3.80e+00 angle pdb=" CA PRO B 642 " pdb=" C PRO B 642 " pdb=" O PRO B 642 " ideal model delta sigma weight residual 118.92 121.13 -2.21 1.14e+00 7.69e-01 3.77e+00 ... (remaining 13117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 5129 17.94 - 35.88: 413 35.88 - 53.82: 65 53.82 - 71.76: 11 71.76 - 89.70: 9 Dihedral angle restraints: 5627 sinusoidal: 2163 harmonic: 3464 Sorted by residual: dihedral pdb=" CA ARG B 595 " pdb=" C ARG B 595 " pdb=" N ASN B 596 " pdb=" CA ASN B 596 " ideal model delta harmonic sigma weight residual 180.00 -150.83 -29.17 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA ALA B 130 " pdb=" C ALA B 130 " pdb=" N PRO B 131 " pdb=" CA PRO B 131 " ideal model delta harmonic sigma weight residual 180.00 158.41 21.59 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA TYR B 339 " pdb=" C TYR B 339 " pdb=" N GLU B 340 " pdb=" CA GLU B 340 " ideal model delta harmonic sigma weight residual 180.00 161.84 18.16 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 5624 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 757 0.026 - 0.052: 404 0.052 - 0.077: 173 0.077 - 0.103: 64 0.103 - 0.129: 14 Chirality restraints: 1412 Sorted by residual: chirality pdb=" CA PRO B 367 " pdb=" N PRO B 367 " pdb=" C PRO B 367 " pdb=" CB PRO B 367 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.15e-01 chirality pdb=" CA ILE B 666 " pdb=" N ILE B 666 " pdb=" C ILE B 666 " pdb=" CB ILE B 666 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.55e-01 chirality pdb=" CA ILE B 364 " pdb=" N ILE B 364 " pdb=" C ILE B 364 " pdb=" CB ILE B 364 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.34e-01 ... (remaining 1409 not shown) Planarity restraints: 1722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 279 " -0.053 5.00e-02 4.00e+02 8.07e-02 1.04e+01 pdb=" N PRO B 280 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 280 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 280 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 509 " -0.026 5.00e-02 4.00e+02 3.97e-02 2.53e+00 pdb=" N PRO A 510 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 510 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 510 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 604 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO A 605 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 605 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 605 " -0.021 5.00e-02 4.00e+02 ... (remaining 1719 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 860 2.74 - 3.28: 9591 3.28 - 3.82: 15292 3.82 - 4.36: 18637 4.36 - 4.90: 32026 Nonbonded interactions: 76406 Sorted by model distance: nonbonded pdb=" O TRP B 91 " pdb=" OH TYR B 98 " model vdw 2.199 2.440 nonbonded pdb=" OH TYR B 113 " pdb=" OD2 ASP B 487 " model vdw 2.236 2.440 nonbonded pdb=" O VAL A 267 " pdb=" OG1 THR A 271 " model vdw 2.256 2.440 nonbonded pdb=" O GLY A 599 " pdb=" ND2 ASN A 602 " model vdw 2.265 2.520 nonbonded pdb=" O TYR B 390 " pdb=" OG1 THR B 394 " model vdw 2.272 2.440 ... (remaining 76401 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 1 7.16 5 S 32 5.16 5 C 5973 2.51 5 N 1622 2.21 5 O 1759 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.890 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: 12.070 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.090 Process input model: 29.950 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 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 : 0.003 0.050 9628 Z= 0.204 Angle : 0.538 7.175 13122 Z= 0.295 Chirality : 0.039 0.129 1412 Planarity : 0.004 0.081 1722 Dihedral : 13.508 89.701 3413 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.24), residues: 1210 helix: 0.27 (0.22), residues: 568 sheet: -1.66 (1.18), residues: 21 loop : -1.50 (0.24), residues: 621 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.194 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.2160 time to fit residues: 22.5405 Evaluate side-chains 52 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.174 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 3.9990 chunk 92 optimal weight: 0.2980 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 0.0770 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 overall best weight: 1.8744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.0644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 9628 Z= 0.306 Angle : 0.526 7.405 13122 Z= 0.258 Chirality : 0.041 0.120 1412 Planarity : 0.004 0.067 1722 Dihedral : 4.876 67.154 1324 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 0.53 % 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: -0.85 (0.24), residues: 1210 helix: 0.45 (0.22), residues: 571 sheet: -1.38 (1.12), residues: 21 loop : -1.53 (0.24), residues: 618 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 1.231 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 54 average time/residue: 0.2073 time to fit residues: 17.0958 Evaluate side-chains 50 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 1.148 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0841 time to fit residues: 2.0087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 109 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 717 GLN B 561 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.0710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 9628 Z= 0.156 Angle : 0.466 7.338 13122 Z= 0.225 Chirality : 0.038 0.122 1412 Planarity : 0.004 0.057 1722 Dihedral : 4.555 72.063 1324 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer Outliers : 0.11 % 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: -0.51 (0.24), residues: 1210 helix: 0.78 (0.23), residues: 573 sheet: -0.70 (1.18), residues: 21 loop : -1.45 (0.24), residues: 616 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 1.160 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 57 average time/residue: 0.1895 time to fit residues: 17.0254 Evaluate side-chains 47 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 1.211 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0935 time to fit residues: 1.6614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 74 optimal weight: 0.1980 chunk 111 optimal weight: 2.9990 chunk 117 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.0800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 9628 Z= 0.272 Angle : 0.509 7.819 13122 Z= 0.247 Chirality : 0.040 0.120 1412 Planarity : 0.004 0.076 1722 Dihedral : 4.679 68.525 1324 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer Outliers : 0.21 % 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: -0.50 (0.24), residues: 1210 helix: 0.79 (0.22), residues: 566 sheet: -0.51 (1.17), residues: 21 loop : -1.42 (0.24), residues: 623 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 1.115 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 53 average time/residue: 0.1966 time to fit residues: 16.4407 Evaluate side-chains 47 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.151 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 9628 Z= 0.268 Angle : 0.507 7.467 13122 Z= 0.246 Chirality : 0.040 0.120 1412 Planarity : 0.004 0.080 1722 Dihedral : 4.722 69.126 1324 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer Outliers : 0.42 % 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: -0.50 (0.24), residues: 1210 helix: 0.78 (0.22), residues: 567 sheet: -0.41 (1.02), residues: 31 loop : -1.43 (0.24), residues: 612 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 1.245 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 56 average time/residue: 0.2007 time to fit residues: 17.8336 Evaluate side-chains 48 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 1.181 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0965 time to fit residues: 1.8903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 9 optimal weight: 0.0970 chunk 39 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 9628 Z= 0.150 Angle : 0.470 7.441 13122 Z= 0.226 Chirality : 0.037 0.121 1412 Planarity : 0.004 0.069 1722 Dihedral : 4.466 73.037 1324 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.29 (0.24), residues: 1210 helix: 0.97 (0.22), residues: 576 sheet: -0.41 (0.99), residues: 33 loop : -1.37 (0.25), residues: 601 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 1.189 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 57 average time/residue: 0.1845 time to fit residues: 16.6710 Evaluate side-chains 46 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 1.191 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0884 time to fit residues: 1.7935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 66 optimal weight: 0.0470 chunk 99 optimal weight: 4.9990 chunk 65 optimal weight: 0.0070 chunk 117 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 9628 Z= 0.187 Angle : 0.486 7.808 13122 Z= 0.233 Chirality : 0.038 0.122 1412 Planarity : 0.004 0.065 1722 Dihedral : 4.462 71.687 1324 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer Outliers : 0.64 % 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 (0.24), residues: 1210 helix: 1.01 (0.22), residues: 576 sheet: -0.35 (0.98), residues: 33 loop : -1.33 (0.25), residues: 601 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 1.191 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 56 average time/residue: 0.1923 time to fit residues: 17.1563 Evaluate side-chains 51 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 1.222 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1348 time to fit residues: 2.1315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 35 optimal weight: 0.0770 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 80 optimal weight: 0.4980 chunk 58 optimal weight: 5.9990 chunk 10 optimal weight: 0.0070 chunk 92 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 9628 Z= 0.157 Angle : 0.480 8.085 13122 Z= 0.229 Chirality : 0.038 0.122 1412 Planarity : 0.004 0.062 1722 Dihedral : 4.400 73.158 1324 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 0.11 % 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: -0.13 (0.24), residues: 1210 helix: 1.13 (0.22), residues: 576 sheet: -0.32 (0.99), residues: 33 loop : -1.33 (0.25), residues: 601 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 1.215 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 0.2029 time to fit residues: 16.4437 Evaluate side-chains 48 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.132 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 71 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 9628 Z= 0.249 Angle : 0.508 7.597 13122 Z= 0.246 Chirality : 0.039 0.121 1412 Planarity : 0.004 0.063 1722 Dihedral : 4.558 70.401 1324 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.24), residues: 1210 helix: 1.07 (0.22), residues: 571 sheet: -0.37 (0.98), residues: 33 loop : -1.40 (0.24), residues: 606 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 1.326 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 53 average time/residue: 0.2221 time to fit residues: 18.8105 Evaluate side-chains 52 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 1.178 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0927 time to fit residues: 2.0682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 9628 Z= 0.174 Angle : 0.488 7.721 13122 Z= 0.235 Chirality : 0.038 0.122 1412 Planarity : 0.004 0.100 1722 Dihedral : 4.453 72.973 1324 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.24), residues: 1210 helix: 1.16 (0.22), residues: 575 sheet: -0.31 (0.98), residues: 33 loop : -1.36 (0.24), residues: 602 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.211 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1918 time to fit residues: 16.3462 Evaluate side-chains 51 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.223 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 602 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.098248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.080806 restraints weight = 17007.636| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.51 r_work: 0.3077 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work: 0.3050 rms_B_bonded: 2.30 restraints_weight: 0.1250 r_work: 0.3036 rms_B_bonded: 2.39 restraints_weight: 0.0625 r_work: 0.3021 rms_B_bonded: 2.52 restraints_weight: 0.0312 r_work: 0.3005 rms_B_bonded: 2.69 restraints_weight: 0.0156 r_work: 0.2988 rms_B_bonded: 2.89 restraints_weight: 0.0078 r_work: 0.2970 rms_B_bonded: 3.13 restraints_weight: 0.0039 r_work: 0.2951 rms_B_bonded: 3.41 restraints_weight: 0.0020 r_work: 0.2930 rms_B_bonded: 3.74 restraints_weight: 0.0010 r_work: 0.2907 rms_B_bonded: 4.11 restraints_weight: 0.0005 r_work: 0.2883 rms_B_bonded: 4.53 restraints_weight: 0.0002 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 9628 Z= 0.291 Angle : 0.528 7.780 13122 Z= 0.257 Chirality : 0.040 0.121 1412 Planarity : 0.004 0.096 1722 Dihedral : 4.658 69.061 1324 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer Outliers : 0.11 % 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: -0.29 (0.24), residues: 1210 helix: 1.02 (0.22), residues: 572 sheet: -0.35 (0.97), residues: 33 loop : -1.42 (0.24), residues: 605 =============================================================================== Job complete usr+sys time: 1689.38 seconds wall clock time: 31 minutes 36.12 seconds (1896.12 seconds total)