Starting phenix.real_space_refine on Fri Mar 15 02:00:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pn1_13545/03_2024/7pn1_13545.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pn1_13545/03_2024/7pn1_13545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pn1_13545/03_2024/7pn1_13545.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pn1_13545/03_2024/7pn1_13545.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pn1_13545/03_2024/7pn1_13545.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pn1_13545/03_2024/7pn1_13545.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 S 32 5.16 5 C 3372 2.51 5 N 828 2.21 5 O 915 1.98 5 H 5237 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 149": "OD1" <-> "OD2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 298": "OD1" <-> "OD2" Residue "A PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 475": "OD1" <-> "OD2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 670": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 679": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10384 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 10384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 10384 Classifications: {'peptide': 657} Link IDs: {'PTRANS': 30, 'TRANS': 626} Chain breaks: 3 Time building chain proxies: 5.30, per 1000 atoms: 0.51 Number of scatterers: 10384 At special positions: 0 Unit cell: (84.15, 92.65, 121.55, 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 32 16.00 O 915 8.00 N 828 7.00 C 3372 6.00 H 5237 1.00 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: 8.20 Conformation dependent library (CDL) restraints added in 1.1 seconds 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1230 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 6 sheets defined 63.2% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 12 through 48 removed outlier: 4.259A pdb=" N PHE A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE A 19 " --> pdb=" O SER A 15 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ALA A 35 " --> pdb=" O TYR A 31 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ILE A 36 " --> pdb=" O GLY A 32 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ASN A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE A 44 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 77 removed outlier: 3.588A pdb=" N ILE A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA A 61 " --> pdb=" O HIS A 57 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 62 " --> pdb=" O THR A 58 " (cutoff:3.500A) Proline residue: A 67 - end of helix removed outlier: 3.853A pdb=" N ILE A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 108 removed outlier: 3.644A pdb=" N ILE A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN A 104 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 139 removed outlier: 3.933A pdb=" N GLY A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A 139 " --> pdb=" O GLY A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 150 removed outlier: 3.608A pdb=" N SER A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN A 150 " --> pdb=" O PHE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 185 Proline residue: A 182 - end of helix removed outlier: 4.203A pdb=" N ARG A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 219 Proline residue: A 205 - end of helix removed outlier: 3.727A pdb=" N GLY A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 223 Processing helix chain 'A' and resid 231 through 249 Processing helix chain 'A' and resid 261 through 266 removed outlier: 3.808A pdb=" N LYS A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 286 removed outlier: 4.037A pdb=" N LEU A 286 " --> pdb=" O ARG A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 298 removed outlier: 3.514A pdb=" N PHE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 310 removed outlier: 4.042A pdb=" N THR A 305 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LEU A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 325 removed outlier: 3.780A pdb=" N MET A 325 " --> pdb=" O PRO A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 343 removed outlier: 4.353A pdb=" N ALA A 330 " --> pdb=" O GLN A 326 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) Proline residue: A 338 - end of helix removed outlier: 3.827A pdb=" N ASP A 341 " --> pdb=" O VAL A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 356 through 383 removed outlier: 3.756A pdb=" N PHE A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 481 through 485 Processing helix chain 'A' and resid 580 through 583 removed outlier: 3.652A pdb=" N LEU A 583 " --> pdb=" O ASN A 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 580 through 583' Processing helix chain 'A' and resid 584 through 610 removed outlier: 4.264A pdb=" N THR A 601 " --> pdb=" O VAL A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 613 No H-bonds generated for 'chain 'A' and resid 611 through 613' Processing helix chain 'A' and resid 614 through 637 removed outlier: 3.822A pdb=" N LEU A 618 " --> pdb=" O MET A 614 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN A 619 " --> pdb=" O LYS A 615 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 626 " --> pdb=" O TRP A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 654 removed outlier: 4.167A pdb=" N PHE A 652 " --> pdb=" O GLU A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 668 Processing helix chain 'A' and resid 670 through 674 removed outlier: 4.436A pdb=" N ASN A 674 " --> pdb=" O THR A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 680 removed outlier: 4.350A pdb=" N ALA A 680 " --> pdb=" O ALA A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 683 No H-bonds generated for 'chain 'A' and resid 681 through 683' Processing sheet with id=AA1, first strand: chain 'A' and resid 422 through 423 Processing sheet with id=AA2, first strand: chain 'A' and resid 422 through 423 removed outlier: 8.777A pdb=" N HIS A 460 " --> pdb=" O GLU A 394 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLN A 396 " --> pdb=" O HIS A 460 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N LEU A 462 " --> pdb=" O GLN A 396 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LYS A 398 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N VAL A 464 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU A 400 " --> pdb=" O VAL A 464 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ALA A 466 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP A 465 " --> pdb=" O HIS A 469 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N HIS A 469 " --> pdb=" O TRP A 465 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 414 through 418 Processing sheet with id=AA4, first strand: chain 'A' and resid 514 through 515 removed outlier: 3.714A pdb=" N ASN A 514 " --> pdb=" O ASN A 492 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 514 through 515 removed outlier: 3.714A pdb=" N ASN A 514 " --> pdb=" O ASN A 492 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLY A 487 " --> pdb=" O TYR A 554 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N TYR A 556 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARG A 489 " --> pdb=" O TYR A 556 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL A 558 " --> pdb=" O ARG A 489 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL A 491 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N ARG A 560 " --> pdb=" O VAL A 491 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA A 553 " --> pdb=" O ASP A 573 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 505 through 510 removed outlier: 6.018A pdb=" N ILE A 498 " --> pdb=" O ASN A 509 " (cutoff:3.500A) 310 hydrogen bonds defined for protein. 885 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: 3.67 Time building geometry restraints manager: 8.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5227 1.03 - 1.23: 11 1.23 - 1.42: 2188 1.42 - 1.62: 3026 1.62 - 1.81: 54 Bond restraints: 10506 Sorted by residual: bond pdb=" N GLY A 602 " pdb=" CA GLY A 602 " ideal model delta sigma weight residual 1.454 1.443 0.011 1.24e-02 6.50e+03 8.33e-01 bond pdb=" N PRO A 536 " pdb=" CA PRO A 536 " ideal model delta sigma weight residual 1.457 1.467 -0.010 1.31e-02 5.83e+03 6.41e-01 bond pdb=" N ILE A 16 " pdb=" CA ILE A 16 " ideal model delta sigma weight residual 1.452 1.461 -0.009 1.18e-02 7.18e+03 6.10e-01 bond pdb=" N CYS A 197 " pdb=" CA CYS A 197 " ideal model delta sigma weight residual 1.457 1.467 -0.011 1.40e-02 5.10e+03 5.89e-01 bond pdb=" CA ILE A 585 " pdb=" CB ILE A 585 " ideal model delta sigma weight residual 1.534 1.540 -0.005 6.80e-03 2.16e+04 5.64e-01 ... (remaining 10501 not shown) Histogram of bond angle deviations from ideal: 100.06 - 106.84: 182 106.84 - 113.63: 12416 113.63 - 120.42: 3627 120.42 - 127.20: 2738 127.20 - 133.99: 54 Bond angle restraints: 19017 Sorted by residual: angle pdb=" C ALA A 637 " pdb=" CA ALA A 637 " pdb=" CB ALA A 637 " ideal model delta sigma weight residual 116.63 110.62 6.01 1.16e+00 7.43e-01 2.68e+01 angle pdb=" CA ALA A 637 " pdb=" C ALA A 637 " pdb=" N GLY A 638 " ideal model delta sigma weight residual 119.63 117.28 2.35 8.10e-01 1.52e+00 8.41e+00 angle pdb=" CA GLY A 79 " pdb=" C GLY A 79 " pdb=" O GLY A 79 " ideal model delta sigma weight residual 122.57 120.35 2.22 9.20e-01 1.18e+00 5.81e+00 angle pdb=" CA MET A 33 " pdb=" CB MET A 33 " pdb=" CG MET A 33 " ideal model delta sigma weight residual 114.10 118.86 -4.76 2.00e+00 2.50e-01 5.67e+00 angle pdb=" N ALA A 637 " pdb=" CA ALA A 637 " pdb=" C ALA A 637 " ideal model delta sigma weight residual 108.08 112.04 -3.96 1.69e+00 3.50e-01 5.49e+00 ... (remaining 19012 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4559 17.98 - 35.96: 291 35.96 - 53.95: 89 53.95 - 71.93: 22 71.93 - 89.91: 10 Dihedral angle restraints: 4971 sinusoidal: 2655 harmonic: 2316 Sorted by residual: dihedral pdb=" CA GLU A 259 " pdb=" C GLU A 259 " pdb=" N HIS A 260 " pdb=" CA HIS A 260 " ideal model delta harmonic sigma weight residual -180.00 -160.13 -19.87 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA LYS A 257 " pdb=" C LYS A 257 " pdb=" N ARG A 258 " pdb=" CA ARG A 258 " ideal model delta harmonic sigma weight residual 180.00 161.68 18.32 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA LEU A 651 " pdb=" C LEU A 651 " pdb=" N PHE A 652 " pdb=" CA PHE A 652 " ideal model delta harmonic sigma weight residual 180.00 162.34 17.66 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 4968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 503 0.027 - 0.053: 196 0.053 - 0.080: 77 0.080 - 0.106: 35 0.106 - 0.133: 16 Chirality restraints: 827 Sorted by residual: chirality pdb=" CA ILE A 535 " pdb=" N ILE A 535 " pdb=" C ILE A 535 " pdb=" CB ILE A 535 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA ILE A 409 " pdb=" N ILE A 409 " pdb=" C ILE A 409 " pdb=" CB ILE A 409 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA ILE A 574 " pdb=" N ILE A 574 " pdb=" C ILE A 574 " pdb=" CB ILE A 574 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.09e-01 ... (remaining 824 not shown) Planarity restraints: 1518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 288 " 0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO A 289 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 289 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 289 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 337 " 0.023 5.00e-02 4.00e+02 3.54e-02 2.01e+00 pdb=" N PRO A 338 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 338 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 338 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 355 " -0.013 2.00e-02 2.50e+03 7.88e-03 1.86e+00 pdb=" CG PHE A 355 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE A 355 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 355 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 355 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 355 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 355 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE A 355 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 355 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 355 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 355 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE A 355 " 0.000 2.00e-02 2.50e+03 ... (remaining 1515 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 1400 2.26 - 2.85: 23508 2.85 - 3.43: 26325 3.43 - 4.02: 35066 4.02 - 4.60: 53279 Nonbonded interactions: 139578 Sorted by model distance: nonbonded pdb=" HZ2 LYS A 398 " pdb=" OD1 ASP A 573 " model vdw 1.677 1.850 nonbonded pdb=" O ILE A 103 " pdb=" HG1 THR A 107 " model vdw 1.689 1.850 nonbonded pdb=" OE1 GLU A 677 " pdb=" H GLU A 677 " model vdw 1.692 1.850 nonbonded pdb=" O GLY A 94 " pdb=" HG1 THR A 98 " model vdw 1.710 1.850 nonbonded pdb=" HG1 THR A 493 " pdb=" O VAL A 558 " model vdw 1.714 1.850 ... (remaining 139573 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: 0.680 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: 0.160 Extract box with map and model: 4.030 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 36.970 Find NCS groups from input model: 0.180 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: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 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 0.023 5269 Z= 0.150 Angle : 0.568 6.005 7156 Z= 0.330 Chirality : 0.038 0.133 827 Planarity : 0.003 0.041 895 Dihedral : 12.954 89.909 1881 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: 1.31 (0.33), residues: 649 helix: 1.85 (0.29), residues: 340 sheet: 0.97 (0.70), residues: 59 loop : -0.50 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 646 HIS 0.006 0.001 HIS A 260 PHE 0.023 0.001 PHE A 355 TYR 0.015 0.001 TYR A 91 ARG 0.003 0.000 ARG A 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 MET cc_start: 0.8958 (mmt) cc_final: 0.8641 (mmt) REVERT: A 485 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7558 (mt-10) REVERT: A 646 TRP cc_start: 0.5906 (t-100) cc_final: 0.5662 (t-100) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.2427 time to fit residues: 27.0272 Evaluate side-chains 63 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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: 0.8037 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5269 Z= 0.193 Angle : 0.545 6.338 7156 Z= 0.294 Chirality : 0.040 0.159 827 Planarity : 0.004 0.041 895 Dihedral : 4.739 19.958 695 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.36 % Allowed : 5.68 % Favored : 93.96 % 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: 1.33 (0.33), residues: 649 helix: 1.92 (0.28), residues: 334 sheet: 1.04 (0.59), residues: 83 loop : -0.72 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 264 HIS 0.005 0.001 HIS A 260 PHE 0.020 0.001 PHE A 24 TYR 0.008 0.001 TYR A 507 ARG 0.001 0.000 ARG A 282 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.7269 (mmt) cc_final: 0.7016 (mmt) REVERT: A 415 MET cc_start: 0.6025 (tpt) cc_final: 0.5794 (tpt) REVERT: A 421 MET cc_start: 0.8970 (mmt) cc_final: 0.8640 (mmt) REVERT: A 485 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7377 (mt-10) outliers start: 2 outliers final: 2 residues processed: 63 average time/residue: 0.2404 time to fit residues: 22.3857 Evaluate side-chains 63 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 211 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 16 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 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: 0.8010 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5269 Z= 0.142 Angle : 0.503 5.361 7156 Z= 0.267 Chirality : 0.039 0.144 827 Planarity : 0.004 0.040 895 Dihedral : 4.580 18.933 695 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.53 % Allowed : 6.22 % Favored : 93.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.33), residues: 649 helix: 1.98 (0.28), residues: 336 sheet: 1.00 (0.59), residues: 83 loop : -0.76 (0.38), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 264 HIS 0.004 0.001 HIS A 260 PHE 0.017 0.001 PHE A 24 TYR 0.010 0.001 TYR A 507 ARG 0.001 0.000 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.7211 (mmt) cc_final: 0.6944 (mmt) REVERT: A 415 MET cc_start: 0.6125 (tpt) cc_final: 0.5908 (tpt) REVERT: A 421 MET cc_start: 0.8970 (mmt) cc_final: 0.8633 (mmt) REVERT: A 485 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7287 (mt-10) outliers start: 3 outliers final: 2 residues processed: 63 average time/residue: 0.2305 time to fit residues: 21.5821 Evaluate side-chains 63 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 380 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- 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: 0.8025 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5269 Z= 0.160 Angle : 0.500 5.289 7156 Z= 0.266 Chirality : 0.039 0.146 827 Planarity : 0.004 0.041 895 Dihedral : 4.502 18.680 695 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.71 % Allowed : 7.28 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.33), residues: 649 helix: 2.10 (0.28), residues: 341 sheet: 0.89 (0.59), residues: 83 loop : -0.79 (0.38), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 264 HIS 0.004 0.001 HIS A 260 PHE 0.017 0.001 PHE A 24 TYR 0.009 0.001 TYR A 507 ARG 0.001 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.7318 (mmt) cc_final: 0.7022 (mmt) REVERT: A 421 MET cc_start: 0.8946 (mmt) cc_final: 0.8599 (mmt) REVERT: A 485 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7279 (mt-10) outliers start: 4 outliers final: 2 residues processed: 66 average time/residue: 0.2325 time to fit residues: 22.7427 Evaluate side-chains 64 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 380 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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: 0.8108 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5269 Z= 0.276 Angle : 0.555 5.318 7156 Z= 0.303 Chirality : 0.040 0.144 827 Planarity : 0.004 0.040 895 Dihedral : 4.666 20.734 695 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.07 % Allowed : 8.35 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.33), residues: 649 helix: 2.03 (0.28), residues: 339 sheet: 0.54 (0.58), residues: 83 loop : -0.77 (0.39), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 264 HIS 0.007 0.002 HIS A 260 PHE 0.019 0.002 PHE A 24 TYR 0.006 0.001 TYR A 12 ARG 0.002 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 MET cc_start: 0.6150 (tpt) cc_final: 0.5885 (tpt) REVERT: A 485 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7488 (mt-10) outliers start: 6 outliers final: 4 residues processed: 66 average time/residue: 0.2322 time to fit residues: 22.6234 Evaluate side-chains 64 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 197 CYS Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 380 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 29 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 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: 0.8048 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5269 Z= 0.143 Angle : 0.499 5.204 7156 Z= 0.264 Chirality : 0.039 0.142 827 Planarity : 0.004 0.041 895 Dihedral : 4.491 18.839 695 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.89 % Allowed : 9.06 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.33), residues: 649 helix: 2.09 (0.28), residues: 347 sheet: 0.55 (0.59), residues: 85 loop : -0.81 (0.39), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 264 HIS 0.005 0.001 HIS A 260 PHE 0.013 0.001 PHE A 44 TYR 0.009 0.001 TYR A 507 ARG 0.001 0.000 ARG A 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.7226 (mmt) cc_final: 0.7011 (mmt) REVERT: A 415 MET cc_start: 0.6199 (tpt) cc_final: 0.5930 (tpt) REVERT: A 485 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7339 (mt-10) outliers start: 5 outliers final: 5 residues processed: 64 average time/residue: 0.2488 time to fit residues: 23.4807 Evaluate side-chains 66 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 197 CYS Chi-restraints excluded: chain A residue 380 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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: 0.8088 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5269 Z= 0.224 Angle : 0.525 5.237 7156 Z= 0.283 Chirality : 0.039 0.135 827 Planarity : 0.004 0.042 895 Dihedral : 4.534 19.387 695 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.07 % Allowed : 9.24 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.33), residues: 649 helix: 2.08 (0.28), residues: 345 sheet: 0.40 (0.58), residues: 85 loop : -0.79 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 264 HIS 0.005 0.001 HIS A 260 PHE 0.014 0.001 PHE A 355 TYR 0.006 0.001 TYR A 91 ARG 0.001 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.7334 (mmt) cc_final: 0.7110 (mmt) REVERT: A 415 MET cc_start: 0.6327 (tpt) cc_final: 0.6053 (tpt) REVERT: A 485 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7453 (mt-10) outliers start: 6 outliers final: 6 residues processed: 67 average time/residue: 0.2793 time to fit residues: 27.4045 Evaluate side-chains 67 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 197 CYS Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 380 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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: 0.8062 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5269 Z= 0.160 Angle : 0.519 5.373 7156 Z= 0.272 Chirality : 0.039 0.141 827 Planarity : 0.004 0.041 895 Dihedral : 4.483 18.467 695 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.89 % Allowed : 9.77 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.33), residues: 649 helix: 2.14 (0.28), residues: 347 sheet: 0.45 (0.58), residues: 85 loop : -0.82 (0.39), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 264 HIS 0.005 0.001 HIS A 260 PHE 0.016 0.001 PHE A 44 TYR 0.010 0.001 TYR A 91 ARG 0.001 0.000 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.7360 (mmt) cc_final: 0.7136 (mmt) REVERT: A 415 MET cc_start: 0.6287 (tpt) cc_final: 0.6027 (tpt) REVERT: A 485 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7339 (mt-10) REVERT: A 679 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8517 (tm-30) outliers start: 5 outliers final: 5 residues processed: 64 average time/residue: 0.2395 time to fit residues: 22.8335 Evaluate side-chains 65 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 197 CYS Chi-restraints excluded: chain A residue 380 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- 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: 0.8057 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5269 Z= 0.158 Angle : 0.513 5.617 7156 Z= 0.270 Chirality : 0.039 0.139 827 Planarity : 0.004 0.042 895 Dihedral : 4.453 18.128 695 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.07 % Allowed : 9.59 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.33), residues: 649 helix: 2.22 (0.28), residues: 346 sheet: 0.42 (0.58), residues: 85 loop : -0.73 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 264 HIS 0.004 0.001 HIS A 260 PHE 0.016 0.001 PHE A 216 TYR 0.013 0.001 TYR A 91 ARG 0.001 0.000 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.7474 (mmt) cc_final: 0.7215 (mmt) REVERT: A 415 MET cc_start: 0.6291 (tpt) cc_final: 0.5948 (tpt) REVERT: A 485 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7337 (mt-10) outliers start: 6 outliers final: 6 residues processed: 66 average time/residue: 0.2510 time to fit residues: 24.3484 Evaluate side-chains 67 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 197 CYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 652 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 15 optimal weight: 0.4980 chunk 47 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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: 0.8037 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5269 Z= 0.145 Angle : 0.513 5.415 7156 Z= 0.268 Chirality : 0.039 0.140 827 Planarity : 0.004 0.042 895 Dihedral : 4.403 17.719 695 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.24 % Allowed : 9.59 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.33), residues: 649 helix: 2.28 (0.28), residues: 346 sheet: 0.47 (0.58), residues: 85 loop : -0.72 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 264 HIS 0.003 0.001 HIS A 260 PHE 0.020 0.001 PHE A 44 TYR 0.009 0.001 TYR A 91 ARG 0.001 0.000 ARG A 272 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.7476 (mmt) cc_final: 0.7235 (mmt) REVERT: A 415 MET cc_start: 0.6291 (tpt) cc_final: 0.5951 (tpt) REVERT: A 485 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7283 (mt-10) outliers start: 7 outliers final: 7 residues processed: 67 average time/residue: 0.2390 time to fit residues: 23.7169 Evaluate side-chains 69 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 62 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 197 CYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 652 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 1.9990 chunk 51 optimal weight: 0.0970 chunk 21 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.107903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.081556 restraints weight = 40874.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.085420 restraints weight = 18050.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.087921 restraints weight = 11340.300| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5269 Z= 0.146 Angle : 0.511 5.164 7156 Z= 0.267 Chirality : 0.039 0.138 827 Planarity : 0.004 0.042 895 Dihedral : 4.352 17.764 695 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.07 % Allowed : 10.30 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.33), residues: 649 helix: 2.35 (0.28), residues: 346 sheet: 0.48 (0.58), residues: 85 loop : -0.70 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 47 HIS 0.003 0.001 HIS A 260 PHE 0.016 0.001 PHE A 216 TYR 0.013 0.001 TYR A 91 ARG 0.001 0.000 ARG A 272 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2523.32 seconds wall clock time: 45 minutes 9.05 seconds (2709.05 seconds total)