Starting phenix.real_space_refine on Thu Dec 7 23:58:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to0_26025/12_2023/7to0_26025.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to0_26025/12_2023/7to0_26025.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to0_26025/12_2023/7to0_26025.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to0_26025/12_2023/7to0_26025.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to0_26025/12_2023/7to0_26025.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to0_26025/12_2023/7to0_26025.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 23 5.49 5 S 33 5.16 5 C 3727 2.51 5 N 1027 2.21 5 O 1178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 249": "OE1" <-> "OE2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 316": "NH1" <-> "NH2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A GLU 373": "OE1" <-> "OE2" Residue "A TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 416": "OD1" <-> "OD2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A ARG 502": "NH1" <-> "NH2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A ASP 529": "OD1" <-> "OD2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A ASP 562": "OD1" <-> "OD2" Residue "A PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 581": "OE1" <-> "OE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 591": "OE1" <-> "OE2" Residue "A ARG 602": "NH1" <-> "NH2" Residue "A GLU 612": "OE1" <-> "OE2" Residue "A GLU 621": "OE1" <-> "OE2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A ASP 641": "OD1" <-> "OD2" Residue "A ASP 683": "OD1" <-> "OD2" Residue "A ASP 705": "OD1" <-> "OD2" Residue "A GLU 716": "OE1" <-> "OE2" Residue "A PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 749": "OE1" <-> "OE2" Residue "A GLU 751": "OE1" <-> "OE2" Residue "A GLU 795": "OE1" <-> "OE2" Residue "A ASP 802": "OD1" <-> "OD2" Residue "A GLU 827": "OE1" <-> "OE2" Residue "A PHE 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 863": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 883": "OE1" <-> "OE2" 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: 5989 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 5479 Classifications: {'peptide': 682} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 653} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 256 Classifications: {'RNA': 12} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 5} Link IDs: {'rna3p': 11} Chain: "C" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 253 Classifications: {'RNA': 12} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 7} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4555 SG CYS A 810 22.813 42.767 28.664 1.00 39.79 S ATOM 4994 SG CYS A 864 21.545 40.805 25.017 1.00 55.33 S ATOM 5033 SG CYS A 869 23.244 44.391 24.842 1.00 53.89 S Time building chain proxies: 3.95, per 1000 atoms: 0.66 Number of scatterers: 5989 At special positions: 0 Unit cell: (97.188, 85.44, 77.964, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 33 16.00 P 23 15.00 O 1178 8.00 N 1027 7.00 C 3727 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: 2.32 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 869 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 810 " 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1300 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 6 sheets defined 47.5% alpha, 6.9% beta 9 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 244 through 252 removed outlier: 3.693A pdb=" N LEU A 248 " --> pdb=" O ARG A 244 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU A 249 " --> pdb=" O ASN A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 282 removed outlier: 4.041A pdb=" N LYS A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR A 271 " --> pdb=" O GLY A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 315 Processing helix chain 'A' and resid 333 through 340 Processing helix chain 'A' and resid 347 through 358 removed outlier: 3.603A pdb=" N GLY A 358 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 377 Processing helix chain 'A' and resid 381 through 396 Processing helix chain 'A' and resid 419 through 434 removed outlier: 3.697A pdb=" N ASP A 425 " --> pdb=" O ASP A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 450 Processing helix chain 'A' and resid 469 through 488 removed outlier: 3.909A pdb=" N TYR A 473 " --> pdb=" O ASP A 469 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE A 474 " --> pdb=" O LYS A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 497 removed outlier: 4.150A pdb=" N SER A 497 " --> pdb=" O GLU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 521 removed outlier: 3.626A pdb=" N VAL A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 558 removed outlier: 3.591A pdb=" N HIS A 557 " --> pdb=" O ILE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 576 Processing helix chain 'A' and resid 580 through 603 removed outlier: 3.689A pdb=" N ASP A 585 " --> pdb=" O GLU A 581 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU A 586 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP A 603 " --> pdb=" O SER A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 625 Processing helix chain 'A' and resid 636 through 649 removed outlier: 3.783A pdb=" N ASP A 641 " --> pdb=" O ARG A 637 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA A 642 " --> pdb=" O ALA A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 684 removed outlier: 3.631A pdb=" N ILE A 681 " --> pdb=" O ALA A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 701 Processing helix chain 'A' and resid 720 through 729 Processing helix chain 'A' and resid 744 through 769 removed outlier: 3.760A pdb=" N ILE A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 794 Processing sheet with id=AA1, first strand: chain 'A' and resid 294 through 296 Processing sheet with id=AA2, first strand: chain 'A' and resid 321 through 322 Processing sheet with id=AA3, first strand: chain 'A' and resid 457 through 460 removed outlier: 6.842A pdb=" N GLN A 457 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU A 740 " --> pdb=" O GLN A 457 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE A 459 " --> pdb=" O LEU A 740 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 816 through 819 removed outlier: 7.293A pdb=" N LEU A 816 " --> pdb=" O CYS A 810 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N CYS A 810 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N CYS A 818 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 831 through 832 Processing sheet with id=AA6, first strand: chain 'A' and resid 842 through 846 removed outlier: 6.652A pdb=" N LYS A 858 " --> pdb=" O LYS A 878 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LYS A 878 " --> pdb=" O LYS A 858 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A 862 " --> pdb=" O GLY A 874 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY A 874 " --> pdb=" O ILE A 862 " (cutoff:3.500A) 243 hydrogen bonds defined for protein. 708 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 23 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 2.02 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1640 1.33 - 1.45: 1039 1.45 - 1.58: 3388 1.58 - 1.70: 45 1.70 - 1.82: 46 Bond restraints: 6158 Sorted by residual: bond pdb=" N VAL A 452 " pdb=" CA VAL A 452 " ideal model delta sigma weight residual 1.459 1.494 -0.035 9.10e-03 1.21e+04 1.51e+01 bond pdb=" CA SER A 891 " pdb=" CB SER A 891 " ideal model delta sigma weight residual 1.524 1.486 0.037 1.31e-02 5.83e+03 8.09e+00 bond pdb=" N ILE A 489 " pdb=" CA ILE A 489 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.22e-02 6.72e+03 8.02e+00 bond pdb=" N ILE A 262 " pdb=" CA ILE A 262 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.95e+00 bond pdb=" N VAL A 414 " pdb=" CA VAL A 414 " ideal model delta sigma weight residual 1.452 1.485 -0.033 1.18e-02 7.18e+03 7.89e+00 ... (remaining 6153 not shown) Histogram of bond angle deviations from ideal: 99.76 - 106.67: 290 106.67 - 113.59: 3380 113.59 - 120.50: 2608 120.50 - 127.41: 2068 127.41 - 134.33: 75 Bond angle restraints: 8421 Sorted by residual: angle pdb=" C THR A 347 " pdb=" N PRO A 348 " pdb=" CA PRO A 348 " ideal model delta sigma weight residual 119.47 127.93 -8.46 1.16e+00 7.43e-01 5.32e+01 angle pdb=" N VAL A 414 " pdb=" CA VAL A 414 " pdb=" C VAL A 414 " ideal model delta sigma weight residual 112.96 107.77 5.19 1.00e+00 1.00e+00 2.69e+01 angle pdb=" N ARG A 316 " pdb=" CA ARG A 316 " pdb=" C ARG A 316 " ideal model delta sigma weight residual 114.75 109.47 5.28 1.26e+00 6.30e-01 1.75e+01 angle pdb=" C THR A 347 " pdb=" CA THR A 347 " pdb=" CB THR A 347 " ideal model delta sigma weight residual 109.31 113.67 -4.36 1.23e+00 6.61e-01 1.26e+01 angle pdb=" N THR A 347 " pdb=" CA THR A 347 " pdb=" C THR A 347 " ideal model delta sigma weight residual 109.62 104.76 4.86 1.45e+00 4.76e-01 1.13e+01 ... (remaining 8416 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 3343 17.65 - 35.30: 304 35.30 - 52.95: 91 52.95 - 70.60: 31 70.60 - 88.25: 14 Dihedral angle restraints: 3783 sinusoidal: 1781 harmonic: 2002 Sorted by residual: dihedral pdb=" O4' G B 12 " pdb=" C1' G B 12 " pdb=" N9 G B 12 " pdb=" C4 G B 12 " ideal model delta sinusoidal sigma weight residual -106.00 -155.28 49.28 1 1.70e+01 3.46e-03 1.15e+01 dihedral pdb=" CA GLY A 659 " pdb=" C GLY A 659 " pdb=" N ILE A 660 " pdb=" CA ILE A 660 " ideal model delta harmonic sigma weight residual -180.00 -163.49 -16.51 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ASP A 822 " pdb=" CB ASP A 822 " pdb=" CG ASP A 822 " pdb=" OD1 ASP A 822 " ideal model delta sinusoidal sigma weight residual -30.00 -85.56 55.56 1 2.00e+01 2.50e-03 1.04e+01 ... (remaining 3780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 543 0.058 - 0.116: 327 0.116 - 0.174: 84 0.174 - 0.232: 1 0.232 - 0.290: 1 Chirality restraints: 956 Sorted by residual: chirality pdb=" CB VAL A 442 " pdb=" CA VAL A 442 " pdb=" CG1 VAL A 442 " pdb=" CG2 VAL A 442 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CB VAL A 453 " pdb=" CA VAL A 453 " pdb=" CG1 VAL A 453 " pdb=" CG2 VAL A 453 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB ILE A 780 " pdb=" CA ILE A 780 " pdb=" CG1 ILE A 780 " pdb=" CG2 ILE A 780 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.87e-01 ... (remaining 953 not shown) Planarity restraints: 994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 9 " -0.025 2.00e-02 2.50e+03 1.30e-02 5.09e+00 pdb=" N9 G B 9 " 0.025 2.00e-02 2.50e+03 pdb=" C8 G B 9 " -0.005 2.00e-02 2.50e+03 pdb=" N7 G B 9 " -0.011 2.00e-02 2.50e+03 pdb=" C5 G B 9 " 0.009 2.00e-02 2.50e+03 pdb=" C6 G B 9 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G B 9 " -0.005 2.00e-02 2.50e+03 pdb=" N1 G B 9 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G B 9 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G B 9 " -0.012 2.00e-02 2.50e+03 pdb=" N3 G B 9 " 0.011 2.00e-02 2.50e+03 pdb=" C4 G B 9 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 566 " 0.026 2.00e-02 2.50e+03 1.45e-02 4.18e+00 pdb=" CG TYR A 566 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR A 566 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A 566 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 566 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 566 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 566 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR A 566 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 7 " -0.024 2.00e-02 2.50e+03 1.03e-02 2.92e+00 pdb=" N9 A B 7 " 0.018 2.00e-02 2.50e+03 pdb=" C8 A B 7 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A B 7 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A B 7 " 0.005 2.00e-02 2.50e+03 pdb=" C6 A B 7 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A B 7 " -0.010 2.00e-02 2.50e+03 pdb=" N1 A B 7 " -0.008 2.00e-02 2.50e+03 pdb=" C2 A B 7 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A B 7 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A B 7 " 0.006 2.00e-02 2.50e+03 ... (remaining 991 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1243 2.81 - 3.33: 5567 3.33 - 3.86: 9870 3.86 - 4.38: 11248 4.38 - 4.90: 19078 Nonbonded interactions: 47006 Sorted by model distance: nonbonded pdb=" O LYS A 723 " pdb=" OG1 THR A 727 " model vdw 2.288 2.440 nonbonded pdb=" O GLU A 503 " pdb=" OG1 THR A 506 " model vdw 2.346 2.440 nonbonded pdb=" O HIS A 557 " pdb=" OH TYR A 715 " model vdw 2.364 2.440 nonbonded pdb=" O PHE A 789 " pdb=" OG SER A 793 " model vdw 2.365 2.440 nonbonded pdb=" OD1 ASP A 392 " pdb=" NH2 ARG A 791 " model vdw 2.414 2.520 ... (remaining 47001 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: 0.670 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: 3.310 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 22.690 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 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 : 0.011 0.045 6158 Z= 0.704 Angle : 1.168 8.457 8421 Z= 0.849 Chirality : 0.069 0.290 956 Planarity : 0.004 0.024 994 Dihedral : 16.218 88.252 2483 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 0.82 % Allowed : 12.66 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.27), residues: 680 helix: -0.59 (0.25), residues: 300 sheet: -3.23 (0.48), residues: 90 loop : -3.09 (0.27), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP A 873 HIS 0.010 0.003 HIS A 876 PHE 0.016 0.004 PHE A 388 TYR 0.026 0.004 TYR A 566 ARG 0.008 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 138 time to evaluate : 0.667 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 142 average time/residue: 0.2153 time to fit residues: 38.6851 Evaluate side-chains 75 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 0.664 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0579 time to fit residues: 1.1414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN A 299 GLN A 305 GLN A 336 GLN A 341 ASN A 349 GLN A 353 ASN A 354 ASN A 381 HIS A 384 ASN A 501 ASN A 517 GLN A 524 GLN A 608 ASN A 619 GLN A 623 HIS A 769 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6158 Z= 0.186 Angle : 0.509 7.683 8421 Z= 0.253 Chirality : 0.038 0.137 956 Planarity : 0.003 0.032 994 Dihedral : 13.698 73.503 1089 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.62 % Allowed : 15.13 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.31), residues: 680 helix: 1.07 (0.29), residues: 306 sheet: -2.81 (0.53), residues: 83 loop : -2.75 (0.30), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 512 HIS 0.007 0.001 HIS A 623 PHE 0.023 0.001 PHE A 685 TYR 0.010 0.001 TYR A 715 ARG 0.003 0.000 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 77 time to evaluate : 0.722 Fit side-chains outliers start: 22 outliers final: 15 residues processed: 89 average time/residue: 0.1646 time to fit residues: 20.2201 Evaluate side-chains 78 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 63 time to evaluate : 0.708 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0629 time to fit residues: 2.6453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- 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: 51.0991 > 50: distance: 91 - 188: 12.488 distance: 94 - 185: 3.072 distance: 131 - 135: 27.409 distance: 135 - 136: 47.267 distance: 136 - 137: 16.619 distance: 136 - 139: 21.928 distance: 137 - 138: 10.611 distance: 137 - 141: 16.823 distance: 139 - 140: 22.456 distance: 141 - 142: 4.259 distance: 142 - 143: 3.210 distance: 142 - 145: 3.848 distance: 143 - 144: 6.040 distance: 143 - 151: 4.737 distance: 145 - 146: 5.634 distance: 146 - 147: 5.563 distance: 146 - 148: 5.586 distance: 147 - 149: 4.690 distance: 148 - 150: 5.321 distance: 149 - 150: 4.651 distance: 152 - 153: 8.892 distance: 152 - 155: 6.718 distance: 153 - 154: 8.465 distance: 153 - 159: 4.452 distance: 155 - 156: 5.948 distance: 156 - 157: 7.577 distance: 156 - 158: 8.353 distance: 159 - 160: 3.112 distance: 160 - 161: 7.026 distance: 160 - 163: 6.668 distance: 161 - 162: 12.277 distance: 161 - 173: 9.400 distance: 163 - 164: 5.078 distance: 164 - 165: 7.548 distance: 164 - 166: 10.851 distance: 165 - 167: 8.196 distance: 166 - 168: 11.679 distance: 166 - 169: 5.311 distance: 167 - 168: 6.206 distance: 168 - 170: 8.967 distance: 169 - 171: 7.230 distance: 170 - 172: 4.629 distance: 171 - 172: 7.555 distance: 173 - 174: 4.134 distance: 174 - 175: 5.145 distance: 175 - 177: 4.102 distance: 177 - 178: 3.732 distance: 177 - 264: 8.747 distance: 178 - 179: 7.646 distance: 178 - 181: 4.414 distance: 179 - 180: 7.242 distance: 179 - 185: 4.102 distance: 180 - 261: 10.332 distance: 181 - 182: 8.869 distance: 181 - 183: 6.117 distance: 182 - 184: 9.795 distance: 186 - 187: 6.952 distance: 186 - 189: 5.652 distance: 187 - 188: 6.934 distance: 187 - 195: 5.753 distance: 189 - 190: 6.923 distance: 190 - 191: 3.755 distance: 190 - 192: 3.371 distance: 191 - 193: 3.404 distance: 192 - 194: 5.258 distance: 193 - 194: 4.775 distance: 195 - 196: 3.851 distance: 195 - 250: 7.429 distance: 196 - 197: 3.314 distance: 196 - 199: 8.925 distance: 197 - 198: 16.106 distance: 197 - 202: 5.739 distance: 198 - 247: 16.649 distance: 199 - 200: 14.611 distance: 199 - 201: 11.834 distance: 203 - 204: 11.718 distance: 203 - 206: 3.965 distance: 204 - 205: 5.488 distance: 204 - 211: 8.313 distance: 206 - 207: 20.180 distance: 207 - 208: 8.756 distance: 208 - 209: 9.162 distance: 209 - 210: 5.855 distance: 212 - 213: 3.653 distance: 212 - 215: 4.760 distance: 213 - 214: 6.759 distance: 213 - 223: 9.028 distance: 215 - 216: 7.948 distance: 216 - 217: 9.526 distance: 216 - 218: 10.617 distance: 217 - 219: 14.477 distance: 218 - 220: 10.786 distance: 219 - 221: 13.704 distance: 220 - 221: 14.985 distance: 221 - 222: 6.511