Starting phenix.real_space_refine on Fri Dec 8 12:55:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ide_35365/12_2023/8ide_35365.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ide_35365/12_2023/8ide_35365.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ide_35365/12_2023/8ide_35365.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ide_35365/12_2023/8ide_35365.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ide_35365/12_2023/8ide_35365.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ide_35365/12_2023/8ide_35365.pdb" } resolution = 3.21 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= -0.001 sd= 0.026 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: 5 Type Number sf(0) Gaussians Mn 1 7.51 5 S 50 5.16 5 C 5244 2.51 5 N 1522 2.21 5 O 1576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 137": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8393 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 929, 6537 Classifications: {'peptide': 929} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 47, 'TRANS': 881} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 316 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 228 Chain: "B" Number of atoms: 1855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1855 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.97, per 1000 atoms: 0.59 Number of scatterers: 8393 At special positions: 0 Unit cell: (76.26, 110.7, 123.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 1 24.99 S 50 16.00 O 1576 8.00 N 1522 7.00 C 5244 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: 3.58 Conformation dependent library (CDL) restraints added in 1.8 seconds 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2132 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 10 sheets defined 46.8% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 93 through 111 removed outlier: 4.682A pdb=" N ALA A 100 " --> pdb=" O ARG A 96 " (cutoff:3.500A) Proline residue: A 101 - end of helix Processing helix chain 'A' and resid 128 through 147 removed outlier: 4.099A pdb=" N ARG A 141 " --> pdb=" O ASP A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 164 Processing helix chain 'A' and resid 205 through 218 Processing helix chain 'A' and resid 225 through 234 Processing helix chain 'A' and resid 237 through 247 Processing helix chain 'A' and resid 263 through 276 removed outlier: 3.713A pdb=" N ALA A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA A 276 " --> pdb=" O ARG A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 309 Processing helix chain 'A' and resid 319 through 323 removed outlier: 3.596A pdb=" N ALA A 322 " --> pdb=" O GLY A 319 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 323 " --> pdb=" O GLY A 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 319 through 323' Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.943A pdb=" N GLY A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 348 Processing helix chain 'A' and resid 351 through 366 removed outlier: 4.335A pdb=" N ILE A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 397 removed outlier: 3.582A pdb=" N VAL A 393 " --> pdb=" O VAL A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 422 Processing helix chain 'A' and resid 442 through 454 Processing helix chain 'A' and resid 467 through 476 removed outlier: 3.950A pdb=" N PHE A 471 " --> pdb=" O SER A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 494 removed outlier: 4.224A pdb=" N CYS A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 516 removed outlier: 3.629A pdb=" N THR A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS A 516 " --> pdb=" O PRO A 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 511 through 516' Processing helix chain 'A' and resid 528 through 538 Processing helix chain 'A' and resid 557 through 565 Processing helix chain 'A' and resid 601 through 607 removed outlier: 4.736A pdb=" N ASP A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A 606 " --> pdb=" O THR A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 666 Processing helix chain 'A' and resid 704 through 714 Processing helix chain 'A' and resid 736 through 743 Processing helix chain 'A' and resid 755 through 762 Processing helix chain 'A' and resid 763 through 773 Processing helix chain 'A' and resid 783 through 795 Processing helix chain 'A' and resid 809 through 813 removed outlier: 3.736A pdb=" N VAL A 813 " --> pdb=" O SER A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 823 removed outlier: 3.870A pdb=" N VAL A 823 " --> pdb=" O LEU A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 839 Processing helix chain 'A' and resid 855 through 865 Processing helix chain 'A' and resid 874 through 888 Processing helix chain 'A' and resid 914 through 916 No H-bonds generated for 'chain 'A' and resid 914 through 916' Processing helix chain 'A' and resid 920 through 933 Processing helix chain 'A' and resid 962 through 981 removed outlier: 3.608A pdb=" N PHE A 967 " --> pdb=" O PRO A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 995 removed outlier: 3.663A pdb=" N ASP A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 762 Processing helix chain 'B' and resid 763 through 772 Processing helix chain 'B' and resid 784 through 795 Processing helix chain 'B' and resid 808 through 815 Processing helix chain 'B' and resid 819 through 823 removed outlier: 3.779A pdb=" N VAL B 823 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 839 Processing helix chain 'B' and resid 856 through 865 Processing helix chain 'B' and resid 874 through 888 Processing helix chain 'B' and resid 914 through 916 No H-bonds generated for 'chain 'B' and resid 914 through 916' Processing helix chain 'B' and resid 919 through 933 Processing helix chain 'B' and resid 962 through 982 removed outlier: 3.818A pdb=" N TYR B 966 " --> pdb=" O TRP B 962 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE B 967 " --> pdb=" O PRO B 963 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA B 982 " --> pdb=" O LEU B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 995 removed outlier: 3.538A pdb=" N HIS B 990 " --> pdb=" O SER B 986 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 123 removed outlier: 6.628A pdb=" N VAL A 122 " --> pdb=" O VAL A 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 340 through 341 removed outlier: 6.048A pdb=" N LEU A 315 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LEU A 175 " --> pdb=" O VAL A 316 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE A 174 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU A 188 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ARG A 197 " --> pdb=" O LEU A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 377 through 379 removed outlier: 3.850A pdb=" N VAL A 377 " --> pdb=" O TYR A 689 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL A 670 " --> pdb=" O LYS A 686 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N TRP A 688 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL A 672 " --> pdb=" O TRP A 688 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG A 725 " --> pdb=" O ILE A 673 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 463 through 464 Processing sheet with id=AA6, first strand: chain 'A' and resid 499 through 500 Processing sheet with id=AA7, first strand: chain 'A' and resid 774 through 775 Processing sheet with id=AA8, first strand: chain 'A' and resid 911 through 912 Processing sheet with id=AA9, first strand: chain 'A' and resid 1004 through 1005 Processing sheet with id=AB1, first strand: chain 'B' and resid 843 through 844 removed outlier: 3.860A pdb=" N LEU B 799 " --> pdb=" O ASP B 843 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG B 774 " --> pdb=" O ILE B 867 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL B 869 " --> pdb=" O ARG B 774 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU B 776 " --> pdb=" O VAL B 869 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU B 892 " --> pdb=" O LYS B 939 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N VAL B 941 " --> pdb=" O LEU B 892 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N SER B 894 " --> pdb=" O VAL B 941 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 942 " --> pdb=" O ARG B 909 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1125 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: 3.08 Time building geometry restraints manager: 3.74 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: 2821 1.34 - 1.46: 843 1.46 - 1.58: 4784 1.58 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 8520 Sorted by residual: bond pdb=" N GLU A 138 " pdb=" CA GLU A 138 " ideal model delta sigma weight residual 1.456 1.482 -0.026 1.28e-02 6.10e+03 4.08e+00 bond pdb=" N ASP A 137 " pdb=" CA ASP A 137 " ideal model delta sigma weight residual 1.457 1.476 -0.020 1.32e-02 5.74e+03 2.20e+00 bond pdb=" C ASP A 137 " pdb=" O ASP A 137 " ideal model delta sigma weight residual 1.236 1.216 0.020 1.35e-02 5.49e+03 2.11e+00 bond pdb=" CB VAL A 316 " pdb=" CG1 VAL A 316 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.83e-01 bond pdb=" CA ILE A 409 " pdb=" CB ILE A 409 " ideal model delta sigma weight residual 1.540 1.527 0.013 1.36e-02 5.41e+03 9.78e-01 ... (remaining 8515 not shown) Histogram of bond angle deviations from ideal: 99.27 - 106.25: 270 106.25 - 113.23: 4853 113.23 - 120.21: 2814 120.21 - 127.19: 3599 127.19 - 134.17: 100 Bond angle restraints: 11636 Sorted by residual: angle pdb=" N GLU A 138 " pdb=" CA GLU A 138 " pdb=" C GLU A 138 " ideal model delta sigma weight residual 113.88 107.08 6.80 1.23e+00 6.61e-01 3.05e+01 angle pdb=" C GLU A 508 " pdb=" CA GLU A 508 " pdb=" CB GLU A 508 " ideal model delta sigma weight residual 117.23 110.21 7.02 1.36e+00 5.41e-01 2.67e+01 angle pdb=" N ASP A 137 " pdb=" CA ASP A 137 " pdb=" C ASP A 137 " ideal model delta sigma weight residual 113.20 108.40 4.80 1.21e+00 6.83e-01 1.58e+01 angle pdb=" C ASP A 396 " pdb=" N ARG A 397 " pdb=" CA ARG A 397 " ideal model delta sigma weight residual 121.80 130.76 -8.96 2.44e+00 1.68e-01 1.35e+01 angle pdb=" CA GLU A 508 " pdb=" C GLU A 508 " pdb=" N LYS A 509 " ideal model delta sigma weight residual 119.98 116.94 3.04 8.50e-01 1.38e+00 1.28e+01 ... (remaining 11631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4692 17.73 - 35.46: 349 35.46 - 53.19: 51 53.19 - 70.92: 15 70.92 - 88.64: 4 Dihedral angle restraints: 5111 sinusoidal: 1793 harmonic: 3318 Sorted by residual: dihedral pdb=" CA CYS A 919 " pdb=" C CYS A 919 " pdb=" N LEU A 920 " pdb=" CA LEU A 920 " ideal model delta harmonic sigma weight residual -180.00 -152.62 -27.38 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA ASP A 917 " pdb=" C ASP A 917 " pdb=" N VAL A 918 " pdb=" CA VAL A 918 " ideal model delta harmonic sigma weight residual -180.00 -156.67 -23.33 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA ALA A 682 " pdb=" C ALA A 682 " pdb=" N ARG A 683 " pdb=" CA ARG A 683 " ideal model delta harmonic sigma weight residual -180.00 -157.94 -22.06 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 5108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1035 0.044 - 0.088: 286 0.088 - 0.132: 90 0.132 - 0.176: 7 0.176 - 0.219: 1 Chirality restraints: 1419 Sorted by residual: chirality pdb=" CG LEU B 974 " pdb=" CB LEU B 974 " pdb=" CD1 LEU B 974 " pdb=" CD2 LEU B 974 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB ILE A 120 " pdb=" CA ILE A 120 " pdb=" CG1 ILE A 120 " pdb=" CG2 ILE A 120 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CB VAL A 736 " pdb=" CA VAL A 736 " pdb=" CG1 VAL A 736 " pdb=" CG2 VAL A 736 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.08e-01 ... (remaining 1416 not shown) Planarity restraints: 1535 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 552 " 0.042 5.00e-02 4.00e+02 6.45e-02 6.65e+00 pdb=" N PRO A 553 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 553 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 553 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 205 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO A 206 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 206 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 206 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 172 " 0.033 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO A 173 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 173 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 173 " 0.028 5.00e-02 4.00e+02 ... (remaining 1532 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.50: 59 2.50 - 3.10: 6579 3.10 - 3.70: 13076 3.70 - 4.30: 17968 4.30 - 4.90: 29436 Nonbonded interactions: 67118 Sorted by model distance: nonbonded pdb=" OD1 ASP A 350 " pdb="MN MN A1101 " model vdw 1.906 2.320 nonbonded pdb=" NE2 HIS A 155 " pdb="MN MN A1101 " model vdw 1.920 2.400 nonbonded pdb=" OD1 ASN A 458 " pdb=" N ASN A 459 " model vdw 2.186 2.520 nonbonded pdb=" C VAL A 99 " pdb=" OE2 GLU A 138 " model vdw 2.253 3.270 nonbonded pdb=" O ARG B 760 " pdb=" NH1 ARG B 994 " model vdw 2.269 2.520 ... (remaining 67113 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: 7.750 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: 27.670 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.400 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 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 0.033 8520 Z= 0.200 Angle : 0.713 10.339 11636 Z= 0.377 Chirality : 0.044 0.219 1419 Planarity : 0.005 0.064 1535 Dihedral : 13.140 88.644 2979 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.52 % Allowed : 14.10 % Favored : 85.38 % Rotamer: Outliers : 0.24 % Allowed : 0.24 % Favored : 99.52 % 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: -1.37 (0.25), residues: 1163 helix: 1.31 (0.23), residues: 497 sheet: -1.07 (0.60), residues: 83 loop : -3.07 (0.24), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 495 HIS 0.011 0.002 HIS B 863 PHE 0.018 0.002 PHE A 172 TYR 0.014 0.002 TYR A 884 ARG 0.003 0.000 ARG A 473 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 203 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 205 average time/residue: 0.2408 time to fit residues: 65.1451 Evaluate side-chains 101 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.961 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 48 optimal weight: 0.0980 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 55 optimal weight: 0.4980 chunk 67 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN A 947 HIS ** A 976 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 976 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8520 Z= 0.255 Angle : 0.703 9.475 11636 Z= 0.357 Chirality : 0.046 0.230 1419 Planarity : 0.005 0.051 1535 Dihedral : 4.890 26.300 1257 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.52 % Allowed : 14.62 % Favored : 84.87 % Rotamer: Outliers : 3.37 % Allowed : 10.71 % Favored : 85.92 % 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: -1.44 (0.25), residues: 1163 helix: 1.19 (0.23), residues: 507 sheet: -1.28 (0.55), residues: 91 loop : -3.12 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 495 HIS 0.010 0.002 HIS A 976 PHE 0.022 0.003 PHE A 370 TYR 0.016 0.001 TYR A 884 ARG 0.004 0.000 ARG B 992 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 109 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 22 residues processed: 129 average time/residue: 0.2067 time to fit residues: 37.3480 Evaluate side-chains 106 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 84 time to evaluate : 0.922 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1003 time to fit residues: 5.3224 ------------------------------------------------------------------------------- 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: 70.046 > 50: distance: 33 - 149: 24.970 distance: 45 - 152: 17.732 distance: 54 - 76: 29.645 distance: 58 - 88: 23.890 distance: 62 - 93: 23.086 distance: 69 - 76: 27.443 distance: 70 - 100: 32.188 distance: 76 - 77: 12.778 distance: 77 - 78: 25.350 distance: 77 - 80: 48.772 distance: 78 - 79: 31.976 distance: 78 - 88: 22.961 distance: 79 - 109: 54.277 distance: 80 - 81: 26.935 distance: 81 - 82: 35.238 distance: 81 - 83: 22.173 distance: 82 - 84: 41.671 distance: 83 - 85: 12.398 distance: 84 - 86: 48.181 distance: 85 - 86: 18.250 distance: 86 - 87: 20.881 distance: 88 - 89: 12.856 distance: 89 - 90: 44.540 distance: 89 - 92: 25.803 distance: 90 - 91: 27.304 distance: 90 - 93: 37.725 distance: 93 - 94: 49.864 distance: 94 - 95: 28.080 distance: 94 - 97: 40.663 distance: 95 - 96: 13.271 distance: 95 - 100: 63.769 distance: 97 - 98: 26.407 distance: 97 - 99: 33.353 distance: 100 - 101: 20.019 distance: 101 - 102: 44.435 distance: 101 - 104: 45.181 distance: 102 - 103: 37.116 distance: 102 - 109: 40.398 distance: 104 - 105: 68.087 distance: 105 - 106: 42.990 distance: 106 - 107: 22.703 distance: 106 - 108: 28.408 distance: 109 - 110: 51.686 distance: 110 - 111: 45.823 distance: 110 - 113: 33.732 distance: 111 - 112: 41.583 distance: 111 - 117: 27.947 distance: 113 - 114: 39.551 distance: 114 - 115: 41.733 distance: 114 - 116: 48.882 distance: 117 - 118: 23.050 distance: 118 - 119: 26.803 distance: 118 - 121: 44.289 distance: 119 - 120: 6.636 distance: 119 - 126: 45.260 distance: 121 - 122: 48.148 distance: 122 - 123: 47.099 distance: 123 - 124: 28.902 distance: 124 - 125: 41.558 distance: 126 - 127: 50.310 distance: 127 - 128: 29.415 distance: 127 - 130: 57.253 distance: 128 - 129: 25.767 distance: 128 - 134: 40.319 distance: 130 - 131: 31.201 distance: 131 - 132: 15.669 distance: 131 - 133: 20.231 distance: 134 - 135: 40.966 distance: 134 - 140: 13.293 distance: 135 - 136: 16.709 distance: 135 - 138: 40.555 distance: 136 - 137: 34.935 distance: 136 - 141: 32.607 distance: 138 - 139: 38.944 distance: 139 - 140: 37.168 distance: 141 - 142: 53.046 distance: 142 - 143: 9.046 distance: 142 - 145: 49.324 distance: 143 - 144: 22.551 distance: 143 - 149: 30.190 distance: 145 - 146: 50.119 distance: 146 - 147: 27.584 distance: 146 - 148: 45.369 distance: 149 - 150: 34.440 distance: 150 - 151: 31.302 distance: 150 - 153: 23.113 distance: 151 - 152: 24.779 distance: 151 - 157: 12.901 distance: 153 - 154: 12.474 distance: 153 - 155: 16.246 distance: 154 - 156: 35.388