Starting phenix.real_space_refine on Fri Aug 2 20:03:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1d_36792/08_2024/8k1d_36792.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1d_36792/08_2024/8k1d_36792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1d_36792/08_2024/8k1d_36792.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1d_36792/08_2024/8k1d_36792.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1d_36792/08_2024/8k1d_36792.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1d_36792/08_2024/8k1d_36792.cif" } resolution = 3.53 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= 0.006 sd= 0.102 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 38 5.16 5 C 3310 2.51 5 N 758 2.21 5 O 796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 682": "OD1" <-> "OD2" Residue "A PHE 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 745": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 777": "OE1" <-> "OE2" Residue "A PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 555": "OE1" <-> "OE2" Residue "B TYR 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 682": "OD1" <-> "OD2" Residue "B PHE 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 745": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 777": "OE1" <-> "OE2" Residue "B ASP 789": "OD1" <-> "OD2" Residue "B PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 4902 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2451 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 297} Chain breaks: 5 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 2451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2451 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 297} Chain breaks: 5 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 32 Time building chain proxies: 3.21, per 1000 atoms: 0.65 Number of scatterers: 4902 At special positions: 0 Unit cell: (93.15, 71.55, 74.25, 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 38 16.00 O 796 8.00 N 758 7.00 C 3310 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 479 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 782 " distance=2.03 Simple disulfide: pdb=" SG CYS B 479 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 782 " distance=2.03 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: 1.94 Conformation dependent library (CDL) restraints added in 879.2 milliseconds 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1164 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 0 sheets defined 83.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 302 through 333 removed outlier: 3.895A pdb=" N TYR A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 474 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'A' and resid 501 through 524 removed outlier: 3.663A pdb=" N VAL A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 565 removed outlier: 4.170A pdb=" N CYS A 565 " --> pdb=" O CYS A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 586 removed outlier: 3.854A pdb=" N GLN A 572 " --> pdb=" O TYR A 568 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE A 573 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE A 577 " --> pdb=" O PHE A 573 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N MET A 578 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 644 removed outlier: 3.615A pdb=" N SER A 644 " --> pdb=" O SER A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 705 Processing helix chain 'A' and resid 708 through 735 Processing helix chain 'A' and resid 744 through 762 removed outlier: 3.893A pdb=" N ALA A 751 " --> pdb=" O ILE A 747 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A 752 " --> pdb=" O VAL A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 778 removed outlier: 3.862A pdb=" N LYS A 778 " --> pdb=" O GLU A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 809 Processing helix chain 'B' and resid 302 through 333 removed outlier: 3.804A pdb=" N TYR B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 474 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 495 through 500 Processing helix chain 'B' and resid 501 through 524 removed outlier: 3.713A pdb=" N VAL B 505 " --> pdb=" O ASN B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 565 removed outlier: 4.145A pdb=" N CYS B 565 " --> pdb=" O CYS B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 586 removed outlier: 3.901A pdb=" N GLN B 572 " --> pdb=" O TYR B 568 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE B 573 " --> pdb=" O SER B 569 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE B 577 " --> pdb=" O PHE B 573 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N MET B 578 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET B 586 " --> pdb=" O ALA B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 644 removed outlier: 3.673A pdb=" N SER B 644 " --> pdb=" O SER B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 705 Processing helix chain 'B' and resid 708 through 735 removed outlier: 3.920A pdb=" N TYR B 712 " --> pdb=" O ASP B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 762 removed outlier: 3.755A pdb=" N ALA B 751 " --> pdb=" O ILE B 747 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL B 752 " --> pdb=" O VAL B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 776 Processing helix chain 'B' and resid 789 through 809 381 hydrogen bonds defined for protein. 1143 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: 1.16 Time building geometry restraints manager: 2.14 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: 1396 1.34 - 1.46: 1174 1.46 - 1.58: 2414 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 5042 Sorted by residual: bond pdb=" C CYS B 565 " pdb=" N PRO B 566 " ideal model delta sigma weight residual 1.335 1.360 -0.025 8.70e-03 1.32e+04 7.99e+00 bond pdb=" C CYS A 565 " pdb=" N PRO A 566 " ideal model delta sigma weight residual 1.334 1.360 -0.026 1.11e-02 8.12e+03 5.39e+00 bond pdb=" N LEU B 512 " pdb=" CA LEU B 512 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.32e+00 bond pdb=" C PRO B 566 " pdb=" O PRO B 566 " ideal model delta sigma weight residual 1.233 1.217 0.016 9.60e-03 1.09e+04 2.76e+00 bond pdb=" C PRO A 566 " pdb=" O PRO A 566 " ideal model delta sigma weight residual 1.233 1.218 0.016 1.06e-02 8.90e+03 2.19e+00 ... (remaining 5037 not shown) Histogram of bond angle deviations from ideal: 98.69 - 105.77: 69 105.77 - 112.85: 2670 112.85 - 119.93: 1776 119.93 - 127.01: 2274 127.01 - 134.09: 57 Bond angle restraints: 6846 Sorted by residual: angle pdb=" C PRO B 566 " pdb=" CA PRO B 566 " pdb=" CB PRO B 566 " ideal model delta sigma weight residual 111.40 108.16 3.24 9.10e-01 1.21e+00 1.27e+01 angle pdb=" CB MET A 554 " pdb=" CG MET A 554 " pdb=" SD MET A 554 " ideal model delta sigma weight residual 112.70 121.74 -9.04 3.00e+00 1.11e-01 9.07e+00 angle pdb=" CA LEU B 802 " pdb=" CB LEU B 802 " pdb=" CG LEU B 802 " ideal model delta sigma weight residual 116.30 125.79 -9.49 3.50e+00 8.16e-02 7.36e+00 angle pdb=" CA TYR A 712 " pdb=" CB TYR A 712 " pdb=" CG TYR A 712 " ideal model delta sigma weight residual 113.90 118.70 -4.80 1.80e+00 3.09e-01 7.12e+00 angle pdb=" CA LEU B 699 " pdb=" CB LEU B 699 " pdb=" CG LEU B 699 " ideal model delta sigma weight residual 116.30 125.01 -8.71 3.50e+00 8.16e-02 6.19e+00 ... (remaining 6841 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.63: 2392 16.63 - 33.25: 338 33.25 - 49.88: 115 49.88 - 66.50: 7 66.50 - 83.13: 4 Dihedral angle restraints: 2856 sinusoidal: 1060 harmonic: 1796 Sorted by residual: dihedral pdb=" CB CYS B 485 " pdb=" SG CYS B 485 " pdb=" SG CYS B 782 " pdb=" CB CYS B 782 " ideal model delta sinusoidal sigma weight residual 93.00 129.34 -36.34 1 1.00e+01 1.00e-02 1.87e+01 dihedral pdb=" CB CYS A 485 " pdb=" SG CYS A 485 " pdb=" SG CYS A 782 " pdb=" CB CYS A 782 " ideal model delta sinusoidal sigma weight residual 93.00 127.81 -34.81 1 1.00e+01 1.00e-02 1.72e+01 dihedral pdb=" CA ASN A 482 " pdb=" C ASN A 482 " pdb=" N PHE A 483 " pdb=" CA PHE A 483 " ideal model delta harmonic sigma weight residual -180.00 -163.30 -16.70 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 2853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 649 0.057 - 0.113: 123 0.113 - 0.170: 15 0.170 - 0.226: 1 0.226 - 0.283: 2 Chirality restraints: 790 Sorted by residual: chirality pdb=" CG LEU B 797 " pdb=" CB LEU B 797 " pdb=" CD1 LEU B 797 " pdb=" CD2 LEU B 797 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CG LEU A 326 " pdb=" CB LEU A 326 " pdb=" CD1 LEU A 326 " pdb=" CD2 LEU A 326 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CG LEU A 797 " pdb=" CB LEU A 797 " pdb=" CD1 LEU A 797 " pdb=" CD2 LEU A 797 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.67e-01 ... (remaining 787 not shown) Planarity restraints: 816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 457 " 0.042 5.00e-02 4.00e+02 6.36e-02 6.48e+00 pdb=" N PRO A 458 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 458 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 458 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 457 " -0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO B 458 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 458 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 458 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 794 " 0.011 2.00e-02 2.50e+03 1.15e-02 3.29e+00 pdb=" CG TRP A 794 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP A 794 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 794 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 794 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 794 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 794 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 794 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 794 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 794 " -0.000 2.00e-02 2.50e+03 ... (remaining 813 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 947 2.76 - 3.30: 5064 3.30 - 3.83: 8108 3.83 - 4.37: 8859 4.37 - 4.90: 15037 Nonbonded interactions: 38015 Sorted by model distance: nonbonded pdb=" O VAL B 469 " pdb=" OG1 THR B 473 " model vdw 2.230 3.040 nonbonded pdb=" OG SER A 644 " pdb=" OH TYR A 724 " model vdw 2.272 3.040 nonbonded pdb=" O ILE B 747 " pdb=" OG1 THR B 750 " model vdw 2.275 3.040 nonbonded pdb=" OG SER B 644 " pdb=" OH TYR B 724 " model vdw 2.286 3.040 nonbonded pdb=" O TRP A 794 " pdb=" OG SER A 798 " model vdw 2.300 3.040 ... (remaining 38010 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.290 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.570 Find NCS groups from input model: 0.120 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:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 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 0.034 5042 Z= 0.186 Angle : 0.714 9.494 6846 Z= 0.370 Chirality : 0.045 0.283 790 Planarity : 0.004 0.064 816 Dihedral : 16.894 83.125 1680 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.57 % Allowed : 27.59 % Favored : 71.84 % 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: 1.26 (0.34), residues: 586 helix: 1.52 (0.22), residues: 478 sheet: None (None), residues: 0 loop : -2.29 (0.58), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 794 HIS 0.003 0.001 HIS B 504 PHE 0.020 0.001 PHE A 745 TYR 0.025 0.001 TYR B 321 ARG 0.003 0.000 ARG B 518 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 113 time to evaluate : 0.500 Fit side-chains REVERT: A 325 LEU cc_start: 0.8445 (tt) cc_final: 0.8109 (mt) REVERT: B 517 ARG cc_start: 0.8342 (ptt90) cc_final: 0.8136 (ptt-90) outliers start: 3 outliers final: 2 residues processed: 115 average time/residue: 0.1333 time to fit residues: 20.6938 Evaluate side-chains 105 residues out of total 538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 727 PHE Chi-restraints excluded: chain A residue 794 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 30.0000 chunk 45 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5042 Z= 0.215 Angle : 0.626 10.410 6846 Z= 0.320 Chirality : 0.041 0.172 790 Planarity : 0.004 0.044 816 Dihedral : 4.586 32.507 654 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.83 % Allowed : 24.71 % Favored : 71.46 % 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: 1.22 (0.33), residues: 586 helix: 1.53 (0.22), residues: 486 sheet: None (None), residues: 0 loop : -2.87 (0.53), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 446 HIS 0.004 0.001 HIS A 504 PHE 0.018 0.002 PHE B 806 TYR 0.017 0.001 TYR B 321 ARG 0.010 0.001 ARG A 517 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 0.556 Fit side-chains REVERT: A 455 TYR cc_start: 0.7125 (t80) cc_final: 0.6634 (t80) REVERT: B 517 ARG cc_start: 0.8338 (ptt90) cc_final: 0.8134 (ptt-90) REVERT: B 580 MET cc_start: 0.8034 (mmt) cc_final: 0.7831 (mmt) REVERT: B 699 LEU cc_start: 0.8912 (mm) cc_final: 0.8640 (pp) REVERT: B 753 MET cc_start: 0.7865 (mmp) cc_final: 0.7566 (mmp) outliers start: 20 outliers final: 11 residues processed: 120 average time/residue: 0.1283 time to fit residues: 20.8864 Evaluate side-chains 109 residues out of total 538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 445 PHE Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 758 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-dev-5409/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-dev-5409/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-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-dev-5409/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-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-dev-5409/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-dev-5409/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-dev-5409/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-dev-5409/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: 53.2871 > 50: distance: 2 - 19: 9.775 distance: 6 - 24: 6.708 distance: 13 - 19: 9.644 distance: 19 - 20: 14.044 distance: 20 - 21: 24.502 distance: 20 - 23: 23.041 distance: 21 - 22: 18.645 distance: 21 - 24: 18.956 distance: 24 - 25: 10.142 distance: 25 - 26: 4.079 distance: 25 - 28: 6.779 distance: 26 - 27: 17.402 distance: 26 - 32: 19.355 distance: 28 - 29: 10.948 distance: 29 - 30: 18.207 distance: 29 - 31: 15.436 distance: 32 - 33: 9.268 distance: 33 - 34: 12.137 distance: 33 - 36: 9.259 distance: 34 - 35: 16.341 distance: 36 - 37: 11.216 distance: 38 - 39: 8.477 distance: 39 - 40: 13.016 distance: 39 - 42: 3.354 distance: 40 - 41: 9.428 distance: 40 - 46: 7.519 distance: 42 - 43: 7.023 distance: 43 - 44: 7.882 distance: 44 - 45: 5.078 distance: 46 - 47: 8.541 distance: 47 - 50: 7.830 distance: 48 - 49: 7.225 distance: 48 - 54: 5.026 distance: 49 - 74: 19.658 distance: 50 - 51: 9.805 distance: 51 - 52: 6.701 distance: 51 - 53: 5.720 distance: 54 - 55: 4.096 distance: 55 - 56: 6.338 distance: 55 - 58: 12.049 distance: 56 - 57: 8.035 distance: 56 - 59: 5.916 distance: 57 - 82: 9.709 distance: 59 - 60: 9.676 distance: 60 - 61: 14.853 distance: 61 - 62: 7.489 distance: 61 - 67: 9.398 distance: 62 - 90: 20.290 distance: 63 - 64: 16.905 distance: 64 - 65: 15.289 distance: 65 - 66: 24.339 distance: 67 - 68: 6.124 distance: 68 - 69: 5.287 distance: 68 - 71: 6.366 distance: 69 - 70: 8.331 distance: 69 - 74: 12.215 distance: 70 - 97: 17.806 distance: 71 - 72: 6.413 distance: 71 - 73: 7.352 distance: 74 - 75: 7.427 distance: 75 - 76: 6.057 distance: 75 - 78: 5.521 distance: 76 - 77: 3.631 distance: 76 - 82: 3.979 distance: 77 - 104: 13.236 distance: 78 - 79: 7.344 distance: 79 - 80: 13.542 distance: 79 - 81: 8.567 distance: 82 - 83: 4.834 distance: 83 - 84: 4.351 distance: 83 - 86: 7.121 distance: 84 - 85: 4.334 distance: 84 - 90: 6.783 distance: 85 - 108: 4.349 distance: 86 - 87: 9.768 distance: 87 - 88: 12.561 distance: 87 - 89: 14.014