Starting phenix.real_space_refine on Thu Dec 7 22:11:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oua_20200/12_2023/6oua_20200.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oua_20200/12_2023/6oua_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_2023/6oua_20200.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oua_20200/12_2023/6oua_20200.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oua_20200/12_2023/6oua_20200.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oua_20200/12_2023/6oua_20200.pdb" } resolution = 4.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 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. 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-1.21rc1-5172/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: 3.30, per 1000 atoms: 0.63 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: 1.87 Conformation dependent library (CDL) restraints added in 929.6 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: 0.46 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: 1.18 Time building geometry restraints manager: 2.04 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 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.740 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 17.690 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 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 : 7.03 Ramachandran Plot: Outliers : 0.32 % Allowed : 17.43 % Favored : 82.25 % Rotamer: Outliers : 2.35 % Allowed : 10.42 % Favored : 87.23 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP I 446 HIS 0.007 0.002 HIS I 678 PHE 0.033 0.003 PHE I 604 TYR 0.022 0.003 TYR I 464 ARG 0.005 0.001 ARG I 697 *********************** 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 : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 147 average time/residue: 0.1970 time to fit residues: 35.9983 Evaluate side-chains 99 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 0.614 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0481 time to fit residues: 1.1851 ------------------------------------------------------------------------------- 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: 0.7650 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 : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.31 % Favored : 86.69 % Rotamer: Outliers : 0.34 % Allowed : 5.21 % Favored : 94.45 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 472 HIS 0.002 0.001 HIS H 111 PHE 0.022 0.002 PHE I 604 TYR 0.016 0.002 TYR H 34 ARG 0.004 0.001 ARG K 119 *********************** 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 : 0.574 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 153 average time/residue: 0.1787 time to fit residues: 34.7963 Evaluate side-chains 99 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 0.574 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0533 time to fit residues: 0.9515 ------------------------------------------------------------------------------- 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: 0.9980 chunk 17 optimal weight: 2.9990 chunk 47 optimal weight: 0.0980 chunk 38 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7640 moved from start: 0.3345 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= 0.189 Angle : 0.737 10.319 7159 Z= 0.371 Chirality : 0.047 0.304 824 Planarity : 0.005 0.099 898 Dihedral : 6.216 48.316 682 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.47 % Favored : 86.53 % Rotamer: Outliers : 0.17 % Allowed : 5.38 % Favored : 94.45 % 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: -3.35 (0.32), residues: 631 helix: -1.08 (0.26), residues: 372 sheet: None (None), residues: 0 loop : -4.05 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 89 HIS 0.001 0.001 HIS I 678 PHE 0.019 0.002 PHE I 604 TYR 0.020 0.001 TYR I 619 ARG 0.003 0.000 ARG K 119 *********************** 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 135 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 0.661 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: 135 average time/residue: 0.1736 time to fit residues: 30.0775 Evaluate side-chains 100 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 0.621 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0535 time to fit residues: 0.9488 ------------------------------------------------------------------------------- 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: 1.9990 chunk 43 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 27 optimal weight: 0.2980 chunk 38 optimal weight: 0.5980 chunk 57 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3663 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= 0.187 Angle : 0.719 8.035 7159 Z= 0.362 Chirality : 0.047 0.250 824 Planarity : 0.005 0.090 898 Dihedral : 5.926 46.964 682 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.63 % Favored : 86.37 % Rotamer: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % 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: -2.82 (0.33), residues: 631 helix: -0.61 (0.27), residues: 372 sheet: None (None), residues: 0 loop : -3.88 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 9 HIS 0.002 0.000 HIS H 57 PHE 0.020 0.001 PHE K 25 TYR 0.013 0.001 TYR H 34 ARG 0.002 0.000 ARG K 119 *********************** 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 127 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1942 time to fit residues: 31.0489 Evaluate side-chains 100 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.627 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8478 ------------------------------------------------------------------------------- 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: 0.7980 chunk 34 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 51 optimal weight: 0.1980 chunk 42 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 490 GLN ** 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: 0.7580 moved from start: 0.3907 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= 0.175 Angle : 0.706 8.875 7159 Z= 0.352 Chirality : 0.045 0.231 824 Planarity : 0.004 0.090 898 Dihedral : 5.741 48.030 682 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.15 % Favored : 86.85 % Rotamer: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % 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: -2.55 (0.34), residues: 631 helix: -0.37 (0.27), residues: 372 sheet: None (None), residues: 0 loop : -3.80 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 89 HIS 0.001 0.000 HIS H 19 PHE 0.019 0.001 PHE K 25 TYR 0.015 0.001 TYR I 711 ARG 0.002 0.000 ARG H 118 *********************** 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 128 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1867 time to fit residues: 30.4711 Evaluate side-chains 96 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.631 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8462 ------------------------------------------------------------------------------- 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: 0.3980 chunk 12 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 28 optimal weight: 0.0670 chunk 5 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 581 GLN ** I 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 677 HIS ** H 62 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.4166 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= 0.179 Angle : 0.729 12.598 7159 Z= 0.358 Chirality : 0.047 0.345 824 Planarity : 0.004 0.092 898 Dihedral : 5.646 49.476 682 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.47 % Favored : 86.53 % Rotamer: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % 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: -2.41 (0.34), residues: 631 helix: -0.24 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -3.86 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 89 HIS 0.007 0.001 HIS I 677 PHE 0.020 0.001 PHE K 25 TYR 0.012 0.001 TYR H 34 ARG 0.003 0.000 ARG H 118 *********************** 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 130 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.666 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: 0.1935 time to fit residues: 31.9609 Evaluate side-chains 107 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.614 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8566 ------------------------------------------------------------------------------- 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: 0.3980 chunk 34 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 28 optimal weight: 0.2980 chunk 24 optimal weight: 0.0970 chunk 36 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7513 moved from start: 0.4540 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= 0.172 Angle : 0.720 11.320 7159 Z= 0.352 Chirality : 0.046 0.319 824 Planarity : 0.004 0.090 898 Dihedral : 5.465 47.536 682 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.00 % Favored : 87.00 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % 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: -2.15 (0.34), residues: 631 helix: -0.06 (0.28), residues: 373 sheet: None (None), residues: 0 loop : -3.63 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 472 HIS 0.003 0.000 HIS H 57 PHE 0.018 0.001 PHE K 25 TYR 0.010 0.001 TYR H 34 ARG 0.004 0.000 ARG H 32 *********************** 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 133 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1805 time to fit residues: 30.6026 Evaluate side-chains 109 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.565 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8684 ------------------------------------------------------------------------------- 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: 0.5980 chunk 41 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 47 optimal weight: 0.0470 chunk 55 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 581 GLN ** I 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4639 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= 0.188 Angle : 0.750 11.192 7159 Z= 0.367 Chirality : 0.048 0.305 824 Planarity : 0.004 0.087 898 Dihedral : 5.443 46.284 682 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.79 % Favored : 86.21 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % 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: -1.99 (0.35), residues: 631 helix: 0.11 (0.28), residues: 373 sheet: None (None), residues: 0 loop : -3.63 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 89 HIS 0.005 0.001 HIS H 57 PHE 0.019 0.002 PHE K 25 TYR 0.020 0.001 TYR I 340 ARG 0.004 0.000 ARG H 32 *********************** 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 124 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1860 time to fit residues: 29.4064 Evaluate side-chains 101 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.572 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.5601 > 50: distance: 80 - 85: 4.978 distance: 85 - 86: 3.749 distance: 86 - 87: 4.919 distance: 86 - 89: 5.298 distance: 87 - 88: 24.488 distance: 87 - 92: 12.250 distance: 89 - 90: 12.925 distance: 89 - 91: 23.693 distance: 92 - 93: 7.983 distance: 93 - 94: 5.533 distance: 93 - 96: 5.883 distance: 94 - 95: 8.230 distance: 94 - 97: 5.765 distance: 97 - 98: 8.738 distance: 98 - 99: 7.639 distance: 98 - 101: 5.380 distance: 99 - 100: 14.292 distance: 99 - 105: 7.105 distance: 101 - 102: 6.565 distance: 102 - 103: 13.542 distance: 102 - 104: 18.647 distance: 105 - 106: 6.584 distance: 106 - 107: 11.616 distance: 106 - 109: 20.515 distance: 107 - 108: 18.391 distance: 107 - 113: 14.571 distance: 109 - 110: 6.056 distance: 110 - 111: 15.100 distance: 110 - 112: 23.222 distance: 113 - 114: 13.188 distance: 114 - 115: 13.086 distance: 114 - 117: 16.246 distance: 115 - 116: 10.379 distance: 115 - 121: 7.134 distance: 117 - 118: 14.244 distance: 117 - 119: 9.080 distance: 118 - 120: 9.620 distance: 121 - 122: 14.307 distance: 122 - 123: 4.608 distance: 122 - 125: 7.146 distance: 123 - 124: 4.302 distance: 123 - 132: 3.225 distance: 125 - 126: 9.265 distance: 126 - 127: 10.149 distance: 127 - 128: 6.343 distance: 128 - 129: 10.145 distance: 129 - 130: 12.054 distance: 129 - 131: 13.073 distance: 132 - 133: 6.803 distance: 133 - 134: 17.544 distance: 133 - 136: 10.049 distance: 134 - 135: 10.504 distance: 134 - 140: 8.057 distance: 136 - 137: 5.762 distance: 137 - 138: 14.975 distance: 137 - 139: 26.351 distance: 140 - 141: 13.878 distance: 141 - 142: 25.665 distance: 141 - 144: 7.171 distance: 142 - 143: 23.786 distance: 142 - 148: 16.132 distance: 144 - 145: 16.365 distance: 145 - 146: 9.052 distance: 145 - 147: 18.622 distance: 148 - 149: 7.541 distance: 149 - 152: 13.038 distance: 150 - 151: 3.601 distance: 150 - 157: 9.133 distance: 152 - 153: 17.329 distance: 153 - 154: 24.174 distance: 154 - 155: 22.214 distance: 154 - 156: 18.849 distance: 157 - 158: 6.489 distance: 158 - 159: 3.679 distance: 158 - 161: 14.813 distance: 159 - 160: 12.525 distance: 159 - 166: 14.858 distance: 162 - 163: 26.692 distance: 163 - 164: 17.332 distance: 164 - 165: 33.164