Starting phenix.real_space_refine on Wed Jan 17 22:06:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sva_25446/01_2024/7sva_25446.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sva_25446/01_2024/7sva_25446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sva_25446/01_2024/7sva_25446.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sva_25446/01_2024/7sva_25446.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sva_25446/01_2024/7sva_25446.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sva_25446/01_2024/7sva_25446.pdb" } resolution = 3.26 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 93 atoms to isotropic. 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 P 11 5.49 5 Mg 1 5.21 5 S 37 5.16 5 C 4090 2.51 5 N 1159 2.21 5 O 1217 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 167": "OE1" <-> "OE2" Residue "A ASP 492": "OD1" <-> "OD2" Residue "A TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 590": "OE1" <-> "OE2" Residue "A GLU 714": "OE1" <-> "OE2" Residue "A GLU 717": "OE1" <-> "OE2" Residue "A PHE 902": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 932": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 6515 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 6290 Classifications: {'peptide': 792} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 747} Chain breaks: 5 Chain: "B" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 224 Classifications: {'DNA': 1, 'RNA': 10} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 5, 'rna3p_pyr': 1} Link IDs: {'rna2p': 4, 'rna3p': 6} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.32, per 1000 atoms: 0.66 Number of scatterers: 6515 At special positions: 0 Unit cell: (77.542, 95.088, 113.766, 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) S 37 16.00 P 11 15.00 Mg 1 11.99 O 1217 8.00 N 1159 7.00 C 4090 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: 2.82 Conformation dependent library (CDL) restraints added in 1.2 seconds 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 8 sheets defined 31.4% alpha, 17.7% beta 0 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 2.14 Creating SS restraints... Processing helix chain 'A' and resid 170 through 186 Processing helix chain 'A' and resid 248 through 257 removed outlier: 3.690A pdb=" N LEU A 252 " --> pdb=" O ASN A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 283 removed outlier: 5.121A pdb=" N LEU A 278 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 357 through 369 Processing helix chain 'A' and resid 460 through 472 removed outlier: 4.205A pdb=" N THR A 465 " --> pdb=" O GLU A 461 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 467 " --> pdb=" O GLN A 463 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A 470 " --> pdb=" O ALA A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 490 removed outlier: 3.731A pdb=" N ALA A 490 " --> pdb=" O VAL A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'A' and resid 565 through 584 Processing helix chain 'A' and resid 602 through 617 Processing helix chain 'A' and resid 637 through 648 Processing helix chain 'A' and resid 658 through 663 Processing helix chain 'A' and resid 665 through 679 removed outlier: 3.671A pdb=" N VAL A 678 " --> pdb=" O LEU A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 770 through 784 removed outlier: 3.703A pdb=" N ASP A 774 " --> pdb=" O GLY A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 821 removed outlier: 3.955A pdb=" N ILE A 813 " --> pdb=" O GLU A 809 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU A 821 " --> pdb=" O CYS A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 915 removed outlier: 3.541A pdb=" N CYS A 915 " --> pdb=" O THR A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing sheet with id=AA1, first strand: chain 'A' and resid 738 through 745 removed outlier: 3.751A pdb=" N ALA A 724 " --> pdb=" O CYS A 743 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ILE A 705 " --> pdb=" O SER A 729 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL A 710 " --> pdb=" O ALA A 795 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE A 790 " --> pdb=" O THR A 829 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ILE A 831 " --> pdb=" O ILE A 790 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N PHE A 792 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL A 833 " --> pdb=" O PHE A 792 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ARG A 794 " --> pdb=" O VAL A 833 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 315 through 318 removed outlier: 3.794A pdb=" N LEU A 322 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN A 503 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 195 through 197 removed outlier: 7.179A pdb=" N GLN A 159 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 241 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS A 214 " --> pdb=" O ILE A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 289 through 291 removed outlier: 4.031A pdb=" N PHE A 311 " --> pdb=" O PHE A 290 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 384 through 387 removed outlier: 3.600A pdb=" N VAL A 373 " --> pdb=" O TYR A 385 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 371 " --> pdb=" O VAL A 387 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 394 removed outlier: 4.665A pdb=" N GLY A 389 " --> pdb=" O GLN A 432 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN A 432 " --> pdb=" O GLY A 389 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR A 391 " --> pdb=" O CYS A 430 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N CYS A 430 " --> pdb=" O THR A 391 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 531 through 532 removed outlier: 3.542A pdb=" N VAL A 686 " --> pdb=" O LYS A 522 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 596 through 597 removed outlier: 4.187A pdb=" N TYR A 596 " --> pdb=" O CYS A 557 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA A 556 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ILE A 629 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL A 558 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N CYS A 656 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA A 628 " --> pdb=" O CYS A 656 " (cutoff:3.500A) 245 hydrogen bonds defined for protein. 708 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 4 stacking parallelities Total time for adding SS restraints: 2.56 Time building geometry restraints manager: 2.99 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: 2082 1.34 - 1.46: 1074 1.46 - 1.58: 3446 1.58 - 1.70: 21 1.70 - 1.81: 52 Bond restraints: 6675 Sorted by residual: bond pdb=" N SER A 720 " pdb=" CA SER A 720 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.29e-02 6.01e+03 6.04e+00 bond pdb=" N GLU A 718 " pdb=" CA GLU A 718 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.20e-02 6.94e+03 4.96e+00 bond pdb=" N ARG A 780 " pdb=" CA ARG A 780 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.19e-02 7.06e+03 4.96e+00 bond pdb=" N SER A 719 " pdb=" CA SER A 719 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 4.95e+00 bond pdb=" N ASN A 715 " pdb=" CA ASN A 715 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.27e+00 ... (remaining 6670 not shown) Histogram of bond angle deviations from ideal: 100.00 - 106.80: 280 106.80 - 113.60: 3659 113.60 - 120.39: 2388 120.39 - 127.19: 2663 127.19 - 133.99: 94 Bond angle restraints: 9084 Sorted by residual: angle pdb=" N TRP A 732 " pdb=" CA TRP A 732 " pdb=" C TRP A 732 " ideal model delta sigma weight residual 109.81 119.53 -9.72 2.21e+00 2.05e-01 1.93e+01 angle pdb=" C LYS A 457 " pdb=" CA LYS A 457 " pdb=" CB LYS A 457 " ideal model delta sigma weight residual 116.34 110.51 5.83 1.40e+00 5.10e-01 1.74e+01 angle pdb=" CA LEU A 368 " pdb=" CB LEU A 368 " pdb=" CG LEU A 368 " ideal model delta sigma weight residual 116.30 127.38 -11.08 3.50e+00 8.16e-02 1.00e+01 angle pdb=" CA GLU A 718 " pdb=" C GLU A 718 " pdb=" O GLU A 718 " ideal model delta sigma weight residual 120.90 117.91 2.99 1.07e+00 8.73e-01 7.81e+00 angle pdb=" CA GLU A 717 " pdb=" C GLU A 717 " pdb=" O GLU A 717 " ideal model delta sigma weight residual 122.32 118.31 4.01 1.51e+00 4.39e-01 7.07e+00 ... (remaining 9079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 3537 16.86 - 33.72: 407 33.72 - 50.58: 83 50.58 - 67.44: 32 67.44 - 84.30: 10 Dihedral angle restraints: 4069 sinusoidal: 1759 harmonic: 2310 Sorted by residual: dihedral pdb=" CA GLY A 856 " pdb=" C GLY A 856 " pdb=" N ASN A 857 " pdb=" CA ASN A 857 " ideal model delta harmonic sigma weight residual 180.00 -160.44 -19.56 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA TRP A 732 " pdb=" C TRP A 732 " pdb=" N PRO A 733 " pdb=" CA PRO A 733 " ideal model delta harmonic sigma weight residual -180.00 -161.75 -18.25 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ASN A 548 " pdb=" C ASN A 548 " pdb=" N GLY A 549 " pdb=" CA GLY A 549 " ideal model delta harmonic sigma weight residual 180.00 162.08 17.92 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 4066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 859 0.056 - 0.112: 143 0.112 - 0.167: 14 0.167 - 0.223: 0 0.223 - 0.279: 1 Chirality restraints: 1017 Sorted by residual: chirality pdb=" CA TRP A 732 " pdb=" N TRP A 732 " pdb=" C TRP A 732 " pdb=" CB TRP A 732 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CB THR A 154 " pdb=" CA THR A 154 " pdb=" OG1 THR A 154 " pdb=" CG2 THR A 154 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.75e-01 chirality pdb=" CB ILE A 701 " pdb=" CA ILE A 701 " pdb=" CG1 ILE A 701 " pdb=" CG2 ILE A 701 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 1014 not shown) Planarity restraints: 1131 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 732 " -0.032 2.00e-02 2.50e+03 2.88e-02 2.07e+01 pdb=" CG TRP A 732 " 0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP A 732 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP A 732 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 732 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 732 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 732 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 732 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 732 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A 732 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 695 " -0.060 5.00e-02 4.00e+02 8.95e-02 1.28e+01 pdb=" N PRO A 696 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO A 696 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 696 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 732 " -0.036 5.00e-02 4.00e+02 5.51e-02 4.85e+00 pdb=" N PRO A 733 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 733 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 733 " -0.031 5.00e-02 4.00e+02 ... (remaining 1128 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 76 2.64 - 3.21: 5713 3.21 - 3.77: 10012 3.77 - 4.34: 13415 4.34 - 4.90: 22923 Nonbonded interactions: 52139 Sorted by model distance: nonbonded pdb=" OD2 ASP A 709 " pdb="MG MG A1001 " model vdw 2.078 2.170 nonbonded pdb=" OD1 ASP A 709 " pdb="MG MG A1001 " model vdw 2.097 2.170 nonbonded pdb=" O ARG A 643 " pdb=" OG1 THR A 647 " model vdw 2.174 2.440 nonbonded pdb=" OG1 THR A 829 " pdb=" OD1 ASN A 900 " model vdw 2.177 2.440 nonbonded pdb=" OE1 GLU A 646 " pdb=" OH TYR A 944 " model vdw 2.192 2.440 ... (remaining 52134 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 7.600 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 23.890 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6675 Z= 0.190 Angle : 0.595 11.079 9084 Z= 0.316 Chirality : 0.041 0.279 1017 Planarity : 0.005 0.089 1131 Dihedral : 15.610 84.303 2575 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.29 % Allowed : 0.29 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.32), residues: 780 helix: 1.87 (0.35), residues: 239 sheet: -1.04 (0.40), residues: 179 loop : -1.39 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.003 TRP A 732 HIS 0.001 0.000 HIS A 427 PHE 0.011 0.001 PHE A 802 TYR 0.007 0.001 TYR A 312 ARG 0.006 0.000 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 57 average time/residue: 0.3552 time to fit residues: 24.4230 Evaluate side-chains 26 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 719 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 24 optimal weight: 0.0170 chunk 38 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 overall best weight: 4.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN A 715 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6675 Z= 0.327 Angle : 0.630 10.015 9084 Z= 0.317 Chirality : 0.043 0.160 1017 Planarity : 0.005 0.058 1131 Dihedral : 10.363 63.936 1021 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.43 % Allowed : 7.53 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.32), residues: 780 helix: 1.96 (0.36), residues: 242 sheet: -0.90 (0.40), residues: 172 loop : -1.37 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 732 HIS 0.003 0.001 HIS A 427 PHE 0.013 0.002 PHE A 211 TYR 0.010 0.001 TYR A 596 ARG 0.007 0.001 ARG A 562 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 34 average time/residue: 0.3610 time to fit residues: 16.0335 Evaluate side-chains 30 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 27 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 717 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 58 optimal weight: 0.0370 chunk 71 optimal weight: 9.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6675 Z= 0.164 Angle : 0.523 7.989 9084 Z= 0.265 Chirality : 0.040 0.151 1017 Planarity : 0.004 0.051 1131 Dihedral : 10.137 63.895 1020 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.29 % Allowed : 9.55 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.32), residues: 780 helix: 2.14 (0.36), residues: 244 sheet: -0.76 (0.39), residues: 177 loop : -1.36 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 732 HIS 0.002 0.001 HIS A 894 PHE 0.011 0.001 PHE A 211 TYR 0.008 0.001 TYR A 596 ARG 0.003 0.000 ARG A 562 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 31 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 615 MET cc_start: 0.7443 (mmm) cc_final: 0.6749 (tpt) outliers start: 2 outliers final: 1 residues processed: 33 average time/residue: 0.2770 time to fit residues: 12.0778 Evaluate side-chains 29 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 717 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 HIS A 489 ASN A 823 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6675 Z= 0.304 Angle : 0.581 6.260 9084 Z= 0.296 Chirality : 0.042 0.147 1017 Planarity : 0.005 0.051 1131 Dihedral : 10.191 63.911 1020 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.59 % Allowed : 10.85 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.31), residues: 780 helix: 2.10 (0.35), residues: 242 sheet: -0.69 (0.40), residues: 163 loop : -1.44 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 732 HIS 0.003 0.001 HIS A 427 PHE 0.010 0.001 PHE A 148 TYR 0.011 0.001 TYR A 596 ARG 0.005 0.001 ARG A 940 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 30 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 41 average time/residue: 0.1776 time to fit residues: 10.6882 Evaluate side-chains 34 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 29 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 945 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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: 59.7025 > 50: distance: 28 - 114: 25.849 distance: 43 - 104: 12.325 distance: 46 - 101: 7.141 distance: 63 - 93: 10.062 distance: 66 - 90: 9.035 distance: 76 - 82: 6.652 distance: 82 - 83: 8.936 distance: 83 - 84: 11.814 distance: 83 - 86: 7.674 distance: 84 - 85: 12.931 distance: 84 - 90: 9.057 distance: 86 - 87: 8.247 distance: 87 - 88: 5.096 distance: 90 - 91: 13.398 distance: 91 - 92: 13.336 distance: 91 - 94: 20.047 distance: 92 - 93: 5.803 distance: 92 - 95: 9.103 distance: 96 - 97: 9.977 distance: 96 - 99: 4.398 distance: 97 - 98: 17.097 distance: 97 - 101: 4.172 distance: 99 - 100: 3.596 distance: 101 - 102: 11.859 distance: 102 - 105: 8.989 distance: 103 - 104: 5.822 distance: 103 - 106: 20.909 distance: 106 - 107: 15.775 distance: 107 - 108: 15.049 distance: 107 - 110: 26.140 distance: 108 - 109: 20.232 distance: 108 - 111: 13.543 distance: 111 - 112: 8.978 distance: 112 - 113: 6.576 distance: 112 - 115: 5.697 distance: 113 - 114: 15.864 distance: 113 - 122: 10.063 distance: 115 - 116: 4.406 distance: 116 - 117: 4.109 distance: 116 - 118: 6.740 distance: 117 - 119: 3.308 distance: 118 - 120: 3.512 distance: 119 - 121: 4.061 distance: 122 - 123: 5.453 distance: 123 - 124: 6.382 distance: 123 - 126: 4.620 distance: 124 - 125: 23.779 distance: 124 - 130: 19.986 distance: 126 - 127: 15.035 distance: 126 - 128: 11.435 distance: 127 - 129: 4.579 distance: 130 - 131: 11.441 distance: 131 - 132: 9.842 distance: 131 - 134: 7.805 distance: 132 - 133: 7.614 distance: 132 - 139: 11.949 distance: 134 - 135: 5.077 distance: 135 - 136: 4.994 distance: 136 - 138: 3.587 distance: 139 - 140: 5.912 distance: 139 - 145: 6.613 distance: 140 - 141: 8.941 distance: 140 - 143: 13.177 distance: 141 - 142: 15.200 distance: 141 - 146: 8.318 distance: 143 - 144: 5.898 distance: 144 - 145: 15.131 distance: 146 - 147: 8.841 distance: 147 - 148: 5.020 distance: 147 - 150: 9.791 distance: 148 - 149: 23.887 distance: 148 - 154: 6.748 distance: 150 - 151: 10.335 distance: 151 - 152: 11.929 distance: 151 - 153: 13.210 distance: 240 - 252: 3.035