Starting phenix.real_space_refine on Sun Jun 8 15:08:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wbv_21599/06_2025/6wbv_21599.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wbv_21599/06_2025/6wbv_21599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wbv_21599/06_2025/6wbv_21599.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wbv_21599/06_2025/6wbv_21599.map" model { file = "/net/cci-nas-00/data/ceres_data/6wbv_21599/06_2025/6wbv_21599.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wbv_21599/06_2025/6wbv_21599.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.013 sd= 0.959 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 3344 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 Co 2 6.85 5 P 2 5.49 5 S 47 5.16 5 C 4398 2.51 5 N 1114 2.21 5 O 1297 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 6860 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 181 Classifications: {'peptide': 25} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 23} 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: 3262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3262 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 418} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "L" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1670 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 4, 'PTRANS': 10, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 1674 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1666 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 220, 1666 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 1703 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' CO': 2, 'AGA': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2181 SG CYS A 326 78.631 63.845 45.666 1.00 49.12 S Time building chain proxies: 6.79, per 1000 atoms: 0.99 Number of scatterers: 6860 At special positions: 0 Unit cell: (113.424, 110.088, 111.756, 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) Co 2 26.99 S 47 16.00 P 2 15.00 O 1297 8.00 N 1114 7.00 C 4398 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS B 7 " - pdb=" SG CYS B 23 " distance=2.03 Simple disulfide: pdb=" SG CYS B 10 " - pdb=" SG CYS B 13 " distance=2.02 Simple disulfide: pdb=" SG CYS B 11 " - pdb=" SG CYS B 19 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 22 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 92 " distance=2.05 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 198 " distance=2.04 Simple disulfide: pdb=" SG CYS L 218 " - pdb=" SG CYS H 133 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS H 145 " - pdb=" SG CYS H 200 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.96 Conformation dependent library (CDL) restraints added in 1.3 seconds 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1650 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 13 sheets defined 47.6% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 17 through 21 Processing helix chain 'A' and resid 23 through 54 Processing helix chain 'A' and resid 58 through 86 removed outlier: 3.503A pdb=" N ALA A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ALA A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ILE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN A 86 " --> pdb=" O TRP A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 Processing helix chain 'A' and resid 116 through 123 Processing helix chain 'A' and resid 125 through 156 removed outlier: 4.247A pdb=" N LEU A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 163 Processing helix chain 'A' and resid 166 through 199 removed outlier: 3.811A pdb=" N LEU A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE A 186 " --> pdb=" O GLN A 182 " (cutoff:3.500A) Proline residue: A 189 - end of helix Processing helix chain 'A' and resid 200 through 230 removed outlier: 3.975A pdb=" N CYS A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 290 through 304 Processing helix chain 'A' and resid 307 through 317 Processing helix chain 'A' and resid 327 through 335 Processing helix chain 'A' and resid 338 through 367 Processing helix chain 'A' and resid 368 through 391 removed outlier: 3.540A pdb=" N LEU A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N CYS A 387 " --> pdb=" O CYS A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 484 removed outlier: 4.491A pdb=" N ILE A 467 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 488 through 514 removed outlier: 3.591A pdb=" N ILE A 512 " --> pdb=" O PHE A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 546 removed outlier: 3.573A pdb=" N GLY A 521 " --> pdb=" O PRO A 517 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 87 Processing helix chain 'L' and resid 125 through 131 Processing helix chain 'L' and resid 187 through 191 Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'H' and resid 205 through 208 Processing sheet with id=AA1, first strand: chain 'B' and resid 7 through 11 Processing sheet with id=AA2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 13 removed outlier: 7.014A pdb=" N MET L 37 " --> pdb=" O TYR L 53 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N TYR L 53 " --> pdb=" O MET L 37 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TRP L 39 " --> pdb=" O LEU L 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 13 removed outlier: 4.141A pdb=" N THR L 101 " --> pdb=" O HIS L 94 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 30 through 31 Processing sheet with id=AA6, first strand: chain 'L' and resid 118 through 122 removed outlier: 5.815A pdb=" N TYR L 177 " --> pdb=" O ASN L 142 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 157 through 159 removed outlier: 4.240A pdb=" N TRP L 152 " --> pdb=" O ARG L 159 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.616A pdb=" N GLN H 66 " --> pdb=" O ASN H 83 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.551A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.987A pdb=" N VAL H 107 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 125 through 129 removed outlier: 5.261A pdb=" N THR H 142 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL H 188 " --> pdb=" O THR H 142 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLY H 144 " --> pdb=" O VAL H 186 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL H 186 " --> pdb=" O GLY H 144 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU H 146 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N SER H 184 " --> pdb=" O LEU H 146 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS H 148 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU H 182 " --> pdb=" O LYS H 148 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 125 through 129 removed outlier: 5.261A pdb=" N THR H 142 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL H 188 " --> pdb=" O THR H 142 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLY H 144 " --> pdb=" O VAL H 186 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL H 186 " --> pdb=" O GLY H 144 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU H 146 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N SER H 184 " --> pdb=" O LEU H 146 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS H 148 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU H 182 " --> pdb=" O LYS H 148 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 156 through 159 470 hydrogen bonds defined for protein. 1308 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: 2.34 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.26: 1060 1.26 - 1.40: 1747 1.40 - 1.55: 4118 1.55 - 1.69: 12 1.69 - 1.83: 68 Bond restraints: 7005 Sorted by residual: bond pdb=" C SER L 32 " pdb=" O SER L 32 " ideal model delta sigma weight residual 1.243 1.122 0.121 9.50e-03 1.11e+04 1.63e+02 bond pdb=" C TYR L 34 " pdb=" O TYR L 34 " ideal model delta sigma weight residual 1.234 1.114 0.120 1.28e-02 6.10e+03 8.84e+01 bond pdb=" CA ALA L 31 " pdb=" C ALA L 31 " ideal model delta sigma weight residual 1.520 1.427 0.093 1.16e-02 7.43e+03 6.44e+01 bond pdb=" CA TYR L 34 " pdb=" C TYR L 34 " ideal model delta sigma weight residual 1.523 1.429 0.094 1.21e-02 6.83e+03 6.10e+01 bond pdb=" C ALA L 31 " pdb=" O ALA L 31 " ideal model delta sigma weight residual 1.235 1.175 0.059 1.13e-02 7.83e+03 2.77e+01 ... (remaining 7000 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 9427 3.30 - 6.60: 101 6.60 - 9.90: 14 9.90 - 13.20: 3 13.20 - 16.49: 2 Bond angle restraints: 9547 Sorted by residual: angle pdb=" C ASN A 516 " pdb=" N PRO A 517 " pdb=" CA PRO A 517 " ideal model delta sigma weight residual 119.28 127.37 -8.09 1.10e+00 8.26e-01 5.41e+01 angle pdb=" C ALA L 55 " pdb=" CA ALA L 55 " pdb=" CB ALA L 55 " ideal model delta sigma weight residual 110.04 100.16 9.88 1.51e+00 4.39e-01 4.28e+01 angle pdb=" O5 AGA A 701 " pdb=" P1 AGA A 701 " pdb=" O6 AGA A 701 " ideal model delta sigma weight residual 93.68 110.17 -16.49 3.00e+00 1.11e-01 3.02e+01 angle pdb=" O5 AGA A 702 " pdb=" P1 AGA A 702 " pdb=" O6 AGA A 702 " ideal model delta sigma weight residual 93.68 109.83 -16.15 3.00e+00 1.11e-01 2.90e+01 angle pdb=" N PRO A 515 " pdb=" CA PRO A 515 " pdb=" C PRO A 515 " ideal model delta sigma weight residual 112.47 121.47 -9.00 2.06e+00 2.36e-01 1.91e+01 ... (remaining 9542 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 3720 17.21 - 34.42: 284 34.42 - 51.63: 96 51.63 - 68.84: 28 68.84 - 86.05: 14 Dihedral angle restraints: 4142 sinusoidal: 1565 harmonic: 2577 Sorted by residual: dihedral pdb=" C SER L 32 " pdb=" N SER L 32 " pdb=" CA SER L 32 " pdb=" CB SER L 32 " ideal model delta harmonic sigma weight residual -122.60 -135.46 12.86 0 2.50e+00 1.60e-01 2.65e+01 dihedral pdb=" C ALA L 55 " pdb=" N ALA L 55 " pdb=" CA ALA L 55 " pdb=" CB ALA L 55 " ideal model delta harmonic sigma weight residual -122.60 -110.94 -11.66 0 2.50e+00 1.60e-01 2.17e+01 dihedral pdb=" CA TYR H 50 " pdb=" C TYR H 50 " pdb=" N ILE H 51 " pdb=" CA ILE H 51 " ideal model delta harmonic sigma weight residual 180.00 158.54 21.46 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 4139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1086 0.111 - 0.221: 33 0.221 - 0.331: 2 0.331 - 0.442: 2 0.442 - 0.552: 1 Chirality restraints: 1124 Sorted by residual: chirality pdb=" CA SER L 32 " pdb=" N SER L 32 " pdb=" C SER L 32 " pdb=" CB SER L 32 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.63e+00 chirality pdb=" CA TRP H 103 " pdb=" N TRP H 103 " pdb=" C TRP H 103 " pdb=" CB TRP H 103 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" CA PRO A 515 " pdb=" N PRO A 515 " pdb=" C PRO A 515 " pdb=" CB PRO A 515 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.36 2.00e-01 2.50e+01 3.19e+00 ... (remaining 1121 not shown) Planarity restraints: 1176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 516 " -0.015 2.00e-02 2.50e+03 2.99e-02 8.95e+00 pdb=" C ASN A 516 " 0.052 2.00e-02 2.50e+03 pdb=" O ASN A 516 " -0.020 2.00e-02 2.50e+03 pdb=" N PRO A 517 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER L 71 " -0.013 2.00e-02 2.50e+03 2.74e-02 7.52e+00 pdb=" C SER L 71 " 0.047 2.00e-02 2.50e+03 pdb=" O SER L 71 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY L 72 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN H 35 " 0.013 2.00e-02 2.50e+03 2.72e-02 7.42e+00 pdb=" C ASN H 35 " -0.047 2.00e-02 2.50e+03 pdb=" O ASN H 35 " 0.018 2.00e-02 2.50e+03 pdb=" N TRP H 36 " 0.016 2.00e-02 2.50e+03 ... (remaining 1173 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 25 2.42 - 3.04: 4166 3.04 - 3.66: 10377 3.66 - 4.28: 16019 4.28 - 4.90: 26508 Nonbonded interactions: 57095 Sorted by model distance: nonbonded pdb="CO CO A 704 " pdb=" O HOH A 806 " model vdw 1.797 2.220 nonbonded pdb=" O THR B 25 " pdb="CO CO A 704 " model vdw 1.798 2.220 nonbonded pdb=" ND2 ASN L 95 " pdb=" O TRP H 103 " model vdw 1.887 3.120 nonbonded pdb=" NE2 HIS A 507 " pdb="CO CO A 704 " model vdw 2.111 2.300 nonbonded pdb=" OG SER A 35 " pdb=" OE1 GLU A 219 " model vdw 2.113 3.040 ... (remaining 57090 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 ========== 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=0.50 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: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.520 Find NCS groups from input model: 0.080 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:13.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 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 : 0.006 0.121 7014 Z= 0.389 Angle : 0.936 16.494 9565 Z= 0.502 Chirality : 0.054 0.552 1124 Planarity : 0.007 0.067 1176 Dihedral : 15.749 86.050 2465 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.26 % Allowed : 9.05 % Favored : 86.68 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 18.42 % 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: -0.54 (0.26), residues: 879 helix: -0.19 (0.22), residues: 382 sheet: 0.01 (0.33), residues: 226 loop : -0.63 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP L 167 HIS 0.005 0.001 HIS L 38 PHE 0.023 0.002 PHE L 75 TYR 0.024 0.002 TYR H 78 ARG 0.009 0.001 ARG H 97 Details of bonding type rmsd hydrogen bonds : bond 0.12386 ( 450) hydrogen bonds : angle 6.04241 ( 1308) SS BOND : bond 0.00872 ( 9) SS BOND : angle 1.24634 ( 18) covalent geometry : bond 0.00648 ( 7005) covalent geometry : angle 0.93528 ( 9547) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.791 Fit side-chains revert: symmetry clash REVERT: A 317 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8696 (mp) REVERT: A 341 ILE cc_start: 0.8536 (mp) cc_final: 0.8291 (mm) REVERT: A 364 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7896 (ttp-110) REVERT: A 366 LYS cc_start: 0.8414 (tppt) cc_final: 0.8202 (mptp) REVERT: A 516 ASN cc_start: 0.7799 (OUTLIER) cc_final: 0.7554 (m-40) REVERT: L 49 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8009 (tptp) REVERT: H 16 GLN cc_start: 0.8131 (mt0) cc_final: 0.7927 (mt0) REVERT: H 216 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6492 (pm20) outliers start: 32 outliers final: 11 residues processed: 157 average time/residue: 0.9847 time to fit residues: 164.3183 Evaluate side-chains 125 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 516 ASN Chi-restraints excluded: chain L residue 49 LYS Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 203 LYS Chi-restraints excluded: chain L residue 218 CYS Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 219 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 50 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 HIS A 86 ASN A 99 GLN A 141 ASN A 155 GLN A 174 ASN A 185 ASN A 481 GLN A 496 GLN L 149 ASN L 194 ASN L 216 ASN H 3 GLN H 77 HIS H 83 ASN H 98 GLN H 196 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.161332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.110398 restraints weight = 16608.246| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.37 r_work: 0.3338 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3207 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7014 Z= 0.178 Angle : 0.634 8.498 9565 Z= 0.334 Chirality : 0.044 0.204 1124 Planarity : 0.006 0.051 1176 Dihedral : 11.181 91.166 1036 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.60 % Allowed : 12.65 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % 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: 1.21 (0.28), residues: 879 helix: 1.70 (0.25), residues: 393 sheet: 0.67 (0.34), residues: 222 loop : -0.34 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 34 HIS 0.004 0.001 HIS A 32 PHE 0.015 0.002 PHE L 213 TYR 0.026 0.002 TYR H 78 ARG 0.003 0.001 ARG H 97 Details of bonding type rmsd hydrogen bonds : bond 0.06417 ( 450) hydrogen bonds : angle 4.56672 ( 1308) SS BOND : bond 0.00783 ( 9) SS BOND : angle 0.99500 ( 18) covalent geometry : bond 0.00397 ( 7005) covalent geometry : angle 0.63335 ( 9547) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8869 (mmtp) cc_final: 0.8434 (mttt) REVERT: A 317 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8652 (mp) REVERT: A 341 ILE cc_start: 0.8551 (mp) cc_final: 0.8277 (mm) REVERT: A 378 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8344 (mp) REVERT: L 49 LYS cc_start: 0.9028 (ttmm) cc_final: 0.8804 (mttt) REVERT: H 16 GLN cc_start: 0.8453 (mt0) cc_final: 0.8138 (mt0) REVERT: H 183 SER cc_start: 0.9014 (p) cc_final: 0.8809 (p) outliers start: 27 outliers final: 14 residues processed: 124 average time/residue: 1.0502 time to fit residues: 138.0335 Evaluate side-chains 114 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain L residue 169 ASP Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 203 LYS Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 219 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 77 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 0.0170 chunk 74 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.162199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.111904 restraints weight = 15336.250| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.28 r_work: 0.3373 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7014 Z= 0.132 Angle : 0.565 9.908 9565 Z= 0.292 Chirality : 0.041 0.172 1124 Planarity : 0.005 0.052 1176 Dihedral : 10.385 84.219 1023 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.33 % Allowed : 15.05 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % 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: 1.90 (0.29), residues: 879 helix: 2.36 (0.26), residues: 393 sheet: 1.08 (0.35), residues: 213 loop : -0.21 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 34 HIS 0.004 0.001 HIS L 94 PHE 0.011 0.002 PHE A 295 TYR 0.024 0.001 TYR H 78 ARG 0.002 0.000 ARG L 112 Details of bonding type rmsd hydrogen bonds : bond 0.05435 ( 450) hydrogen bonds : angle 4.25847 ( 1308) SS BOND : bond 0.00556 ( 9) SS BOND : angle 0.85864 ( 18) covalent geometry : bond 0.00280 ( 7005) covalent geometry : angle 0.56466 ( 9547) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8857 (mmtp) cc_final: 0.8447 (mttt) REVERT: A 317 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8724 (mp) REVERT: A 341 ILE cc_start: 0.8548 (mp) cc_final: 0.8283 (mm) REVERT: L 49 LYS cc_start: 0.8966 (ttmm) cc_final: 0.8739 (mttt) REVERT: H 16 GLN cc_start: 0.8356 (mt0) cc_final: 0.8021 (mt0) REVERT: H 183 SER cc_start: 0.9044 (p) cc_final: 0.8840 (p) outliers start: 25 outliers final: 13 residues processed: 120 average time/residue: 1.1118 time to fit residues: 140.9320 Evaluate side-chains 117 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain L residue 169 ASP Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 219 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 65 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.159114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.109496 restraints weight = 10846.326| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.95 r_work: 0.3346 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3251 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3251 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 7014 Z= 0.203 Angle : 0.640 10.293 9565 Z= 0.332 Chirality : 0.045 0.223 1124 Planarity : 0.005 0.051 1176 Dihedral : 10.330 83.423 1018 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.26 % Allowed : 14.65 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % 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: 1.84 (0.28), residues: 879 helix: 2.25 (0.25), residues: 393 sheet: 1.17 (0.35), residues: 213 loop : -0.23 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 34 HIS 0.004 0.001 HIS L 94 PHE 0.013 0.002 PHE A 295 TYR 0.026 0.002 TYR H 78 ARG 0.004 0.000 ARG H 97 Details of bonding type rmsd hydrogen bonds : bond 0.06585 ( 450) hydrogen bonds : angle 4.45585 ( 1308) SS BOND : bond 0.00835 ( 9) SS BOND : angle 2.01818 ( 18) covalent geometry : bond 0.00469 ( 7005) covalent geometry : angle 0.63419 ( 9547) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.743 Fit side-chains revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8850 (mmtp) cc_final: 0.8422 (mttt) REVERT: A 317 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8679 (mp) REVERT: A 341 ILE cc_start: 0.8577 (mp) cc_final: 0.8245 (mm) REVERT: A 364 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7811 (ttp-110) REVERT: L 18 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7464 (ptm160) REVERT: L 43 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8377 (mttt) REVERT: L 49 LYS cc_start: 0.9015 (ttmm) cc_final: 0.8738 (mttt) REVERT: H 16 GLN cc_start: 0.8358 (mt0) cc_final: 0.8026 (mt0) outliers start: 32 outliers final: 20 residues processed: 121 average time/residue: 1.1185 time to fit residues: 142.8380 Evaluate side-chains 124 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 43 LYS Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 203 LYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 219 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.158249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.107032 restraints weight = 16801.214| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.33 r_work: 0.3291 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 7014 Z= 0.272 Angle : 0.701 10.660 9565 Z= 0.365 Chirality : 0.048 0.247 1124 Planarity : 0.006 0.057 1176 Dihedral : 10.505 83.169 1018 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.66 % Allowed : 14.78 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % 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: 1.69 (0.28), residues: 879 helix: 2.06 (0.25), residues: 394 sheet: 1.25 (0.35), residues: 213 loop : -0.39 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 34 HIS 0.004 0.001 HIS A 535 PHE 0.014 0.002 PHE A 295 TYR 0.029 0.002 TYR H 78 ARG 0.005 0.001 ARG L 112 Details of bonding type rmsd hydrogen bonds : bond 0.07293 ( 450) hydrogen bonds : angle 4.64234 ( 1308) SS BOND : bond 0.00957 ( 9) SS BOND : angle 1.93366 ( 18) covalent geometry : bond 0.00639 ( 7005) covalent geometry : angle 0.69624 ( 9547) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8882 (mmtp) cc_final: 0.8440 (mttt) REVERT: A 296 ARG cc_start: 0.8511 (mtm180) cc_final: 0.8060 (mtt-85) REVERT: A 317 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8744 (mp) REVERT: A 364 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.7933 (ttp-110) REVERT: L 18 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7433 (ptm160) REVERT: L 43 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8605 (mttt) REVERT: L 49 LYS cc_start: 0.9080 (ttmm) cc_final: 0.8823 (mttt) REVERT: H 16 GLN cc_start: 0.8398 (mt0) cc_final: 0.8070 (mt0) outliers start: 35 outliers final: 23 residues processed: 126 average time/residue: 1.1522 time to fit residues: 153.1567 Evaluate side-chains 125 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 43 LYS Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 203 LYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 219 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.161027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.109677 restraints weight = 20068.212| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.53 r_work: 0.3325 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7014 Z= 0.155 Angle : 0.591 10.427 9565 Z= 0.306 Chirality : 0.042 0.200 1124 Planarity : 0.005 0.049 1176 Dihedral : 10.154 79.677 1018 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.60 % Allowed : 16.38 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % 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: 1.95 (0.29), residues: 879 helix: 2.38 (0.26), residues: 393 sheet: 1.30 (0.35), residues: 212 loop : -0.32 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 34 HIS 0.004 0.001 HIS A 32 PHE 0.012 0.002 PHE A 26 TYR 0.024 0.002 TYR H 78 ARG 0.003 0.000 ARG L 112 Details of bonding type rmsd hydrogen bonds : bond 0.05877 ( 450) hydrogen bonds : angle 4.33525 ( 1308) SS BOND : bond 0.00707 ( 9) SS BOND : angle 1.62092 ( 18) covalent geometry : bond 0.00345 ( 7005) covalent geometry : angle 0.58745 ( 9547) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.712 Fit side-chains revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8851 (mmtp) cc_final: 0.8453 (mttt) REVERT: A 296 ARG cc_start: 0.8457 (mtm180) cc_final: 0.8018 (mtt-85) REVERT: A 317 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8723 (mp) REVERT: L 18 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7451 (ptm160) REVERT: L 49 LYS cc_start: 0.9047 (ttmm) cc_final: 0.8777 (mttt) REVERT: L 182 THR cc_start: 0.8157 (m) cc_final: 0.7722 (t) REVERT: H 16 GLN cc_start: 0.8335 (mt0) cc_final: 0.8004 (mt0) outliers start: 27 outliers final: 19 residues processed: 115 average time/residue: 1.1193 time to fit residues: 135.9262 Evaluate side-chains 116 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 366 LYS Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 203 LYS Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 219 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 25 optimal weight: 0.7980 chunk 45 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.160927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.110126 restraints weight = 16537.265| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.33 r_work: 0.3334 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7014 Z= 0.161 Angle : 0.594 10.683 9565 Z= 0.307 Chirality : 0.043 0.213 1124 Planarity : 0.005 0.048 1176 Dihedral : 9.943 76.741 1018 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.99 % Allowed : 16.64 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % 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: 2.01 (0.29), residues: 879 helix: 2.41 (0.25), residues: 393 sheet: 1.38 (0.35), residues: 212 loop : -0.31 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 34 HIS 0.004 0.001 HIS A 32 PHE 0.012 0.002 PHE A 26 TYR 0.025 0.002 TYR H 78 ARG 0.003 0.000 ARG L 112 Details of bonding type rmsd hydrogen bonds : bond 0.05964 ( 450) hydrogen bonds : angle 4.32374 ( 1308) SS BOND : bond 0.00665 ( 9) SS BOND : angle 1.36064 ( 18) covalent geometry : bond 0.00360 ( 7005) covalent geometry : angle 0.59174 ( 9547) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8859 (mmtp) cc_final: 0.8451 (mttt) REVERT: A 296 ARG cc_start: 0.8460 (mtm180) cc_final: 0.8020 (mtt-85) REVERT: A 317 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8686 (mp) REVERT: L 18 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7452 (ptm160) REVERT: L 49 LYS cc_start: 0.9044 (ttmm) cc_final: 0.8779 (mttt) REVERT: L 182 THR cc_start: 0.8169 (m) cc_final: 0.7734 (t) REVERT: H 16 GLN cc_start: 0.8297 (mt0) cc_final: 0.7952 (mt0) outliers start: 30 outliers final: 23 residues processed: 119 average time/residue: 1.1328 time to fit residues: 142.4807 Evaluate side-chains 120 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 366 LYS Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 203 LYS Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 83 ASN Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 219 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.6537 > 50: distance: 32 - 38: 23.852 distance: 38 - 39: 27.699 distance: 39 - 40: 17.008 distance: 39 - 42: 5.524 distance: 40 - 41: 8.505 distance: 40 - 46: 36.847 distance: 42 - 43: 27.243 distance: 42 - 44: 16.407 distance: 43 - 45: 18.491 distance: 46 - 47: 10.550 distance: 47 - 48: 21.300 distance: 47 - 50: 8.388 distance: 48 - 49: 21.297 distance: 48 - 55: 23.723 distance: 50 - 51: 37.455 distance: 51 - 52: 19.971 distance: 52 - 53: 25.386 distance: 53 - 54: 17.014 distance: 55 - 56: 13.295 distance: 56 - 59: 5.626 distance: 57 - 58: 14.042 distance: 59 - 60: 3.891 distance: 60 - 61: 10.437 distance: 61 - 62: 4.103 distance: 62 - 63: 3.486 distance: 63 - 64: 5.372 distance: 63 - 65: 3.702 distance: 66 - 67: 8.709 distance: 67 - 68: 14.750 distance: 67 - 70: 8.213 distance: 68 - 69: 6.798 distance: 68 - 71: 23.352 distance: 71 - 72: 22.785 distance: 72 - 73: 12.254 distance: 72 - 75: 17.540 distance: 73 - 74: 17.868 distance: 73 - 79: 11.697 distance: 75 - 76: 14.178 distance: 76 - 77: 8.043 distance: 76 - 78: 9.091 distance: 79 - 80: 24.108 distance: 80 - 81: 17.311 distance: 80 - 83: 25.001 distance: 81 - 82: 29.636 distance: 81 - 84: 5.691 distance: 84 - 85: 5.919 distance: 85 - 86: 30.726 distance: 85 - 88: 24.331 distance: 86 - 87: 20.568 distance: 86 - 89: 9.326 distance: 89 - 90: 14.675 distance: 89 - 95: 26.432 distance: 90 - 91: 45.163 distance: 90 - 93: 27.466 distance: 91 - 96: 31.935 distance: 93 - 94: 25.187 distance: 94 - 95: 24.885 distance: 96 - 97: 18.867 distance: 96 - 130: 23.234 distance: 97 - 98: 7.517 distance: 97 - 100: 18.064 distance: 98 - 99: 8.805 distance: 98 - 103: 17.194 distance: 99 - 127: 18.325 distance: 100 - 101: 8.350 distance: 100 - 102: 31.637 distance: 103 - 104: 7.136 distance: 104 - 105: 12.456 distance: 104 - 107: 15.976 distance: 105 - 106: 8.783 distance: 105 - 110: 14.619 distance: 107 - 108: 3.476 distance: 107 - 109: 8.840