Starting phenix.real_space_refine (version: dev) on Sun Dec 11 16:23:02 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oua_20200/12_2022/6oua_20200.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oua_20200/12_2022/6oua_20200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oua_20200/12_2022/6oua_20200.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oua_20200/12_2022/6oua_20200.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oua_20200/12_2022/6oua_20200.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oua_20200/12_2022/6oua_20200.pdb" } resolution = 4.18 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= 0.003 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 "I ARG 506": "NH1" <-> "NH2" Residue "I TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 712": "NH1" <-> "NH2" Residue "H ARG 56": "NH1" <-> "NH2" Residue "H ARG 118": "NH1" <-> "NH2" Residue "K ARG 39": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 5208 Number of models: 1 Model: "" Number of chains: 3 Chain: "I" Number of atoms: 3105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3105 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 12, 'TRANS': 369} Chain: "H" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1100 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "K" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1003 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Time building chain proxies: 3.58, per 1000 atoms: 0.69 Number of scatterers: 5208 At special positions: 0 Unit cell: (111.35, 88.4, 77.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 958 8.00 N 885 7.00 C 3340 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 763.1 milliseconds 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1240 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 0 sheets defined 62.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'I' and resid 342 through 348 removed outlier: 4.690A pdb=" N ASN I 348 " --> pdb=" O ILE I 344 " (cutoff:3.500A) Processing helix chain 'I' and resid 354 through 368 removed outlier: 3.809A pdb=" N GLU I 358 " --> pdb=" O SER I 354 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE I 361 " --> pdb=" O TYR I 357 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE I 368 " --> pdb=" O LEU I 364 " (cutoff:3.500A) Processing helix chain 'I' and resid 374 through 377 removed outlier: 4.248A pdb=" N GLU I 377 " --> pdb=" O THR I 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 374 through 377' Processing helix chain 'I' and resid 378 through 386 Processing helix chain 'I' and resid 389 through 397 removed outlier: 5.069A pdb=" N ARG I 395 " --> pdb=" O LYS I 391 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE I 396 " --> pdb=" O LEU I 392 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE I 397 " --> pdb=" O SER I 393 " (cutoff:3.500A) Processing helix chain 'I' and resid 412 through 420 Processing helix chain 'I' and resid 432 through 448 removed outlier: 3.922A pdb=" N VAL I 437 " --> pdb=" O ARG I 433 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LYS I 438 " --> pdb=" O GLU I 434 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TRP I 446 " --> pdb=" O SER I 442 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR I 448 " --> pdb=" O PHE I 444 " (cutoff:3.500A) Processing helix chain 'I' and resid 458 through 475 removed outlier: 4.032A pdb=" N THR I 470 " --> pdb=" O LEU I 466 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN I 471 " --> pdb=" O GLN I 467 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP I 475 " --> pdb=" O ASN I 471 " (cutoff:3.500A) Processing helix chain 'I' and resid 478 through 494 removed outlier: 3.944A pdb=" N THR I 484 " --> pdb=" O ALA I 480 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N HIS I 487 " --> pdb=" O LEU I 483 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASP I 488 " --> pdb=" O THR I 484 " (cutoff:3.500A) Processing helix chain 'I' and resid 508 through 525 removed outlier: 4.190A pdb=" N LEU I 519 " --> pdb=" O SER I 515 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN I 525 " --> pdb=" O GLN I 521 " (cutoff:3.500A) Processing helix chain 'I' and resid 531 through 535 Processing helix chain 'I' and resid 550 through 565 removed outlier: 3.908A pdb=" N LEU I 554 " --> pdb=" O ASP I 550 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU I 561 " --> pdb=" O ALA I 557 " (cutoff:3.500A) Processing helix chain 'I' and resid 578 through 593 removed outlier: 4.246A pdb=" N ASN I 590 " --> pdb=" O MET I 586 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 613 Processing helix chain 'I' and resid 614 through 618 removed outlier: 3.821A pdb=" N ASN I 617 " --> pdb=" O ILE I 614 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU I 618 " --> pdb=" O LEU I 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 614 through 618' Processing helix chain 'I' and resid 625 through 630 removed outlier: 3.868A pdb=" N LYS I 629 " --> pdb=" O PHE I 625 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE I 630 " --> pdb=" O LYS I 626 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 625 through 630' Processing helix chain 'I' and resid 641 through 653 removed outlier: 3.955A pdb=" N ARG I 649 " --> pdb=" O ILE I 645 " (cutoff:3.500A) Processing helix chain 'I' and resid 668 through 675 Processing helix chain 'I' and resid 692 through 697 Processing helix chain 'I' and resid 697 through 705 removed outlier: 4.891A pdb=" N HIS I 703 " --> pdb=" O LYS I 699 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER I 705 " --> pdb=" O LEU I 701 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 39 removed outlier: 3.669A pdb=" N ILE H 28 " --> pdb=" O ARG H 24 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASP H 31 " --> pdb=" O LEU H 27 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TYR H 34 " --> pdb=" O LEU H 30 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU H 35 " --> pdb=" O ASP H 31 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS H 39 " --> pdb=" O LEU H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 66 removed outlier: 4.148A pdb=" N ARG H 56 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS H 57 " --> pdb=" O LEU H 53 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE H 61 " --> pdb=" O HIS H 57 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR H 66 " --> pdb=" O ASN H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 90 Processing helix chain 'H' and resid 102 through 129 removed outlier: 3.802A pdb=" N SER H 108 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG H 118 " --> pdb=" O LEU H 114 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU H 120 " --> pdb=" O GLU H 116 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ARG H 121 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU H 123 " --> pdb=" O ALA H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 132 No H-bonds generated for 'chain 'H' and resid 130 through 132' Processing helix chain 'K' and resid 6 through 32 removed outlier: 4.036A pdb=" N LYS K 13 " --> pdb=" O ASP K 9 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN K 18 " --> pdb=" O ASN K 14 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 38 removed outlier: 3.693A pdb=" N THR K 37 " --> pdb=" O ASP K 34 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS K 38 " --> pdb=" O GLU K 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 34 through 38' Processing helix chain 'K' and resid 49 through 57 removed outlier: 3.515A pdb=" N THR K 54 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N GLU K 55 " --> pdb=" O GLU K 51 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU K 56 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU K 57 " --> pdb=" O PHE K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 75 removed outlier: 3.554A pdb=" N LEU K 74 " --> pdb=" O GLY K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 107 removed outlier: 4.432A pdb=" N SER K 91 " --> pdb=" O SER K 87 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU K 105 " --> pdb=" O LYS K 101 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU K 106 " --> pdb=" O ALA K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 128 removed outlier: 3.595A pdb=" N ASP K 113 " --> pdb=" O ASN K 109 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS K 115 " --> pdb=" O ASN K 111 " (cutoff:3.500A) 218 hydrogen bonds defined for protein. 645 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.33 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1546 1.34 - 1.45: 867 1.45 - 1.57: 2850 1.57 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 5305 Sorted by residual: bond pdb=" CA PHE I 630 " pdb=" CB PHE I 630 " ideal model delta sigma weight residual 1.524 1.480 0.044 1.33e-02 5.65e+03 1.08e+01 bond pdb=" CB GLU H 16 " pdb=" CG GLU H 16 " ideal model delta sigma weight residual 1.520 1.444 0.076 3.00e-02 1.11e+03 6.49e+00 bond pdb=" C LYS K 46 " pdb=" N PRO K 47 " ideal model delta sigma weight residual 1.334 1.386 -0.053 2.34e-02 1.83e+03 5.04e+00 bond pdb=" N ASP I 351 " pdb=" CA ASP I 351 " ideal model delta sigma weight residual 1.457 1.486 -0.028 1.29e-02 6.01e+03 4.76e+00 bond pdb=" CB LEU I 466 " pdb=" CG LEU I 466 " ideal model delta sigma weight residual 1.530 1.490 0.040 2.00e-02 2.50e+03 4.02e+00 ... (remaining 5300 not shown) Histogram of bond angle deviations from ideal: 98.48 - 105.59: 83 105.59 - 112.69: 2683 112.69 - 119.80: 2031 119.80 - 126.90: 2293 126.90 - 134.01: 69 Bond angle restraints: 7159 Sorted by residual: angle pdb=" C CYS I 401 " pdb=" N ASN I 402 " pdb=" CA ASN I 402 " ideal model delta sigma weight residual 121.54 130.86 -9.32 1.91e+00 2.74e-01 2.38e+01 angle pdb=" C ASP I 389 " pdb=" N ASN I 390 " pdb=" CA ASN I 390 " ideal model delta sigma weight residual 121.54 130.30 -8.76 1.91e+00 2.74e-01 2.11e+01 angle pdb=" CA LEU H 90 " pdb=" CB LEU H 90 " pdb=" CG LEU H 90 " ideal model delta sigma weight residual 116.30 132.18 -15.88 3.50e+00 8.16e-02 2.06e+01 angle pdb=" CA ILE I 620 " pdb=" CB ILE I 620 " pdb=" CG2 ILE I 620 " ideal model delta sigma weight residual 110.50 118.10 -7.60 1.70e+00 3.46e-01 2.00e+01 angle pdb=" C HIS H 41 " pdb=" N ALA H 42 " pdb=" CA ALA H 42 " ideal model delta sigma weight residual 121.54 130.01 -8.47 1.91e+00 2.74e-01 1.97e+01 ... (remaining 7154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.45: 2859 15.45 - 30.90: 297 30.90 - 46.36: 71 46.36 - 61.81: 14 61.81 - 77.26: 6 Dihedral angle restraints: 3247 sinusoidal: 1354 harmonic: 1893 Sorted by residual: dihedral pdb=" CA ILE I 636 " pdb=" C ILE I 636 " pdb=" N PRO I 637 " pdb=" CA PRO I 637 " ideal model delta harmonic sigma weight residual -180.00 -119.27 -60.73 0 5.00e+00 4.00e-02 1.48e+02 dihedral pdb=" CA ASP K 68 " pdb=" C ASP K 68 " pdb=" N PRO K 69 " pdb=" CA PRO K 69 " ideal model delta harmonic sigma weight residual 180.00 152.87 27.13 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA TYR I 340 " pdb=" C TYR I 340 " pdb=" N SER I 341 " pdb=" CA SER I 341 " ideal model delta harmonic sigma weight residual 180.00 154.12 25.88 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 3244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 679 0.088 - 0.177: 125 0.177 - 0.265: 17 0.265 - 0.353: 2 0.353 - 0.442: 1 Chirality restraints: 824 Sorted by residual: chirality pdb=" CB ILE K 36 " pdb=" CA ILE K 36 " pdb=" CG1 ILE K 36 " pdb=" CG2 ILE K 36 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.88e+00 chirality pdb=" CB ILE I 636 " pdb=" CA ILE I 636 " pdb=" CG1 ILE I 636 " pdb=" CG2 ILE I 636 " both_signs ideal model delta sigma weight residual False 2.64 2.98 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CB ILE H 44 " pdb=" CA ILE H 44 " pdb=" CG1 ILE H 44 " pdb=" CG2 ILE H 44 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 821 not shown) Planarity restraints: 898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE I 636 " 0.060 5.00e-02 4.00e+02 9.20e-02 1.36e+01 pdb=" N PRO I 637 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO I 637 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO I 637 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP K 68 " 0.044 5.00e-02 4.00e+02 6.54e-02 6.85e+00 pdb=" N PRO K 69 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO K 69 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO K 69 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP I 550 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO I 551 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO I 551 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO I 551 " 0.035 5.00e-02 4.00e+02 ... (remaining 895 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 1512 2.82 - 3.34: 4911 3.34 - 3.86: 7947 3.86 - 4.38: 8702 4.38 - 4.90: 14301 Nonbonded interactions: 37373 Sorted by model distance: nonbonded pdb=" O LEU I 552 " pdb=" OG SER I 555 " model vdw 2.294 2.440 nonbonded pdb=" NH2 ARG H 118 " pdb=" OE1 GLN K 107 " model vdw 2.309 2.520 nonbonded pdb=" OD1 ASP I 549 " pdb=" OG1 THR I 634 " model vdw 2.312 2.440 nonbonded pdb=" OD2 ASP H 31 " pdb=" NH2 ARG H 56 " model vdw 2.322 2.520 nonbonded pdb=" NH2 ARG H 71 " pdb=" OD2 ASP K 68 " model vdw 2.331 2.520 ... (remaining 37368 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: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 3340 2.51 5 N 885 2.21 5 O 958 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=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: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.960 Check model and map are aligned: 0.090 Convert atoms to be neutral: 0.050 Process input model: 18.430 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.076 5305 Z= 0.496 Angle : 1.373 15.883 7159 Z= 0.694 Chirality : 0.071 0.442 824 Planarity : 0.008 0.092 898 Dihedral : 13.972 77.258 2007 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.32 % Allowed : 17.43 % Favored : 82.25 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: -5.89 (0.23), residues: 631 helix: -3.43 (0.17), residues: 371 sheet: None (None), residues: 0 loop : -4.59 (0.31), residues: 260 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 138 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 147 average time/residue: 0.1877 time to fit residues: 34.5430 Evaluate side-chains 99 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 0.620 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0478 time to fit residues: 1.1913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 26 optimal weight: 0.0870 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 371 GLN I 581 GLN I 666 ASN ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 GLN H 111 HIS ** K 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 5305 Z= 0.197 Angle : 0.753 7.732 7159 Z= 0.387 Chirality : 0.047 0.227 824 Planarity : 0.006 0.100 898 Dihedral : 6.744 51.840 682 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.31 % Favored : 86.69 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: -4.30 (0.29), residues: 631 helix: -1.94 (0.23), residues: 372 sheet: None (None), residues: 0 loop : -4.27 (0.33), residues: 259 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 151 time to evaluate : 0.626 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 153 average time/residue: 0.1772 time to fit residues: 34.4482 Evaluate side-chains 99 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 0.651 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0507 time to fit residues: 1.0023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 0.0770 chunk 17 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 19 optimal weight: 0.0770 chunk 45 optimal weight: 0.8980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 487 HIS ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 5305 Z= 0.191 Angle : 0.740 10.301 7159 Z= 0.373 Chirality : 0.047 0.306 824 Planarity : 0.005 0.098 898 Dihedral : 6.245 48.761 682 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.47 % Favored : 86.53 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: -3.44 (0.31), residues: 631 helix: -1.16 (0.25), residues: 379 sheet: None (None), residues: 0 loop : -4.13 (0.35), residues: 252 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 133 average time/residue: 0.1760 time to fit residues: 30.0923 Evaluate side-chains 102 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 0.667 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0577 time to fit residues: 1.0943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 0.4980 chunk 43 optimal weight: 5.9990 chunk 29 optimal weight: 0.1980 chunk 6 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 0.0030 chunk 60 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 54 optimal weight: 0.0770 chunk 16 optimal weight: 2.9990 overall best weight: 0.3550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 595 ASN ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 5305 Z= 0.168 Angle : 0.710 7.908 7159 Z= 0.354 Chirality : 0.046 0.248 824 Planarity : 0.005 0.089 898 Dihedral : 5.821 46.983 682 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.68 % Favored : 87.32 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.33), residues: 631 helix: -0.58 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -3.85 (0.36), residues: 260 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1818 time to fit residues: 31.1717 Evaluate side-chains 102 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.712 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 45 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 54 optimal weight: 0.0000 chunk 15 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 490 GLN ** I 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 5305 Z= 0.178 Angle : 0.700 8.987 7159 Z= 0.348 Chirality : 0.045 0.236 824 Planarity : 0.004 0.089 898 Dihedral : 5.670 46.838 682 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.84 % Favored : 87.16 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.34), residues: 631 helix: -0.20 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -3.76 (0.37), residues: 259 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1821 time to fit residues: 30.5254 Evaluate side-chains 99 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.673 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 0.0770 chunk 12 optimal weight: 0.6980 chunk 35 optimal weight: 7.9990 chunk 15 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 20 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 677 HIS ** K 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 5305 Z= 0.173 Angle : 0.727 12.484 7159 Z= 0.357 Chirality : 0.047 0.343 824 Planarity : 0.004 0.091 898 Dihedral : 5.622 49.598 682 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.63 % Favored : 86.37 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.34), residues: 631 helix: -0.07 (0.28), residues: 373 sheet: None (None), residues: 0 loop : -3.68 (0.37), residues: 258 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1776 time to fit residues: 29.4127 Evaluate side-chains 106 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.678 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 581 GLN ** H 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 21 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 5305 Z= 0.221 Angle : 0.753 11.532 7159 Z= 0.372 Chirality : 0.048 0.320 824 Planarity : 0.005 0.090 898 Dihedral : 5.697 46.578 682 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.95 % Favored : 86.05 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.34), residues: 631 helix: 0.02 (0.28), residues: 375 sheet: None (None), residues: 0 loop : -3.65 (0.37), residues: 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1942 time to fit residues: 31.2319 Evaluate side-chains 99 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.667 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 47 optimal weight: 0.0270 chunk 55 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 5305 Z= 0.202 Angle : 0.772 11.154 7159 Z= 0.379 Chirality : 0.049 0.302 824 Planarity : 0.005 0.090 898 Dihedral : 5.673 48.265 682 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.79 % Favored : 86.21 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.34), residues: 631 helix: -0.00 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -3.60 (0.37), residues: 260 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1782 time to fit residues: 29.3557 Evaluate side-chains 97 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.682 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 51 optimal weight: 0.0870 chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 0.0980 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 overall best weight: 0.5160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 5305 Z= 0.184 Angle : 0.767 12.004 7159 Z= 0.372 Chirality : 0.048 0.298 824 Planarity : 0.005 0.087 898 Dihedral : 5.555 46.041 682 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.00 % Favored : 87.00 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.34), residues: 631 helix: 0.11 (0.28), residues: 371 sheet: None (None), residues: 0 loop : -3.64 (0.37), residues: 260 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1806 time to fit residues: 30.0877 Evaluate side-chains 100 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.855 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 1.9990 chunk 57 optimal weight: 0.0050 chunk 49 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 5305 Z= 0.184 Angle : 0.779 13.210 7159 Z= 0.373 Chirality : 0.048 0.296 824 Planarity : 0.004 0.084 898 Dihedral : 5.521 45.842 682 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.68 % Favored : 87.32 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: -1.89 (0.35), residues: 631 helix: 0.16 (0.28), residues: 377 sheet: None (None), residues: 0 loop : -3.60 (0.37), residues: 254 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1709 time to fit residues: 29.1927 Evaluate side-chains 102 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.619 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 0.0980 chunk 50 optimal weight: 6.9990 chunk 20 optimal weight: 0.0870 chunk 51 optimal weight: 0.2980 chunk 6 optimal weight: 0.1980 chunk 9 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.0170 chunk 33 optimal weight: 1.9990 overall best weight: 0.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.166963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.150298 restraints weight = 8430.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.152979 restraints weight = 5609.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.154956 restraints weight = 4083.067| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.5276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 5305 Z= 0.174 Angle : 0.779 12.900 7159 Z= 0.370 Chirality : 0.047 0.299 824 Planarity : 0.004 0.081 898 Dihedral : 5.381 43.406 682 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.25 % Favored : 88.75 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: -1.80 (0.35), residues: 631 helix: 0.26 (0.28), residues: 373 sheet: None (None), residues: 0 loop : -3.54 (0.37), residues: 258 =============================================================================== Job complete usr+sys time: 1440.25 seconds wall clock time: 26 minutes 50.02 seconds (1610.02 seconds total)