Starting phenix.real_space_refine on Fri Oct 11 06:48:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pr1_13607/10_2024/7pr1_13607.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pr1_13607/10_2024/7pr1_13607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pr1_13607/10_2024/7pr1_13607.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pr1_13607/10_2024/7pr1_13607.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pr1_13607/10_2024/7pr1_13607.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pr1_13607/10_2024/7pr1_13607.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.124 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 26 5.16 5 C 5888 2.51 5 N 1604 2.21 5 O 1696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 9222 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4579 Classifications: {'peptide': 587} Link IDs: {'PTRANS': 17, 'TRANS': 569} Chain: "B" Number of atoms: 4579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4579 Classifications: {'peptide': 587} Link IDs: {'PTRANS': 17, 'TRANS': 569} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.59, per 1000 atoms: 0.61 Number of scatterers: 9222 At special positions: 0 Unit cell: (74.048, 90.688, 139.776, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 26 16.00 P 6 15.00 Mg 2 11.99 O 1696 8.00 N 1604 7.00 C 5888 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 - 3.00 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: 2.70 Conformation dependent library (CDL) restraints added in 1.1 seconds 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2192 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 6 sheets defined 73.2% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 92 through 101 removed outlier: 3.874A pdb=" N ILE A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 110 through 146 Proline residue: A 134 - end of helix Processing helix chain 'A' and resid 147 through 149 No H-bonds generated for 'chain 'A' and resid 147 through 149' Processing helix chain 'A' and resid 159 through 205 removed outlier: 4.152A pdb=" N SER A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 214 Processing helix chain 'A' and resid 215 through 240 removed outlier: 3.925A pdb=" N THR A 220 " --> pdb=" O THR A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 259 removed outlier: 3.501A pdb=" N THR A 244 " --> pdb=" O HIS A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 309 removed outlier: 4.184A pdb=" N ALA A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LYS A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N PHE A 288 " --> pdb=" O TRP A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 318 through 372 removed outlier: 3.573A pdb=" N PHE A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 400 Proline residue: A 393 - end of helix Processing helix chain 'A' and resid 400 through 420 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 504 through 508 removed outlier: 3.777A pdb=" N VAL A 508 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 516 Processing helix chain 'A' and resid 530 through 537 Processing helix chain 'A' and resid 543 through 554 Processing helix chain 'A' and resid 556 through 563 Processing helix chain 'A' and resid 565 through 569 Processing helix chain 'A' and resid 572 through 576 Processing helix chain 'A' and resid 579 through 595 Processing helix chain 'A' and resid 609 through 628 Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 660 through 668 Processing helix chain 'A' and resid 669 through 677 Processing helix chain 'B' and resid 93 through 101 Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 110 through 146 Proline residue: B 134 - end of helix Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 159 through 205 removed outlier: 4.152A pdb=" N SER B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 215 through 240 removed outlier: 3.925A pdb=" N THR B 220 " --> pdb=" O THR B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 259 removed outlier: 3.501A pdb=" N THR B 244 " --> pdb=" O HIS B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 309 removed outlier: 4.184A pdb=" N ALA B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LYS B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N PHE B 288 " --> pdb=" O TRP B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 316 Processing helix chain 'B' and resid 318 through 372 removed outlier: 3.574A pdb=" N PHE B 346 " --> pdb=" O THR B 342 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER B 349 " --> pdb=" O ALA B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 400 Proline residue: B 393 - end of helix Processing helix chain 'B' and resid 400 through 420 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 504 through 508 removed outlier: 3.777A pdb=" N VAL B 508 " --> pdb=" O ILE B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 516 Processing helix chain 'B' and resid 530 through 537 Processing helix chain 'B' and resid 543 through 554 Processing helix chain 'B' and resid 556 through 563 Processing helix chain 'B' and resid 565 through 569 Processing helix chain 'B' and resid 572 through 576 Processing helix chain 'B' and resid 579 through 595 Processing helix chain 'B' and resid 609 through 628 Processing helix chain 'B' and resid 637 through 641 Processing helix chain 'B' and resid 660 through 668 Processing helix chain 'B' and resid 669 through 677 Processing sheet with id=AA1, first strand: chain 'A' and resid 457 through 460 removed outlier: 5.435A pdb=" N ARG A 458 " --> pdb=" O PHE A 448 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N PHE A 448 " --> pdb=" O ARG A 458 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 460 removed outlier: 5.435A pdb=" N ARG A 458 " --> pdb=" O PHE A 448 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N PHE A 448 " --> pdb=" O ARG A 458 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL A 446 " --> pdb=" O GLN A 495 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLN A 495 " --> pdb=" O VAL A 446 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 517 through 520 removed outlier: 6.611A pdb=" N LEU A 599 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL A 634 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N PHE A 601 " --> pdb=" O VAL A 634 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LYS A 469 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ILE A 648 " --> pdb=" O LYS A 469 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA A 471 " --> pdb=" O ILE A 648 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU A 650 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL A 473 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU A 657 " --> pdb=" O VAL A 649 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS A 651 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N VAL A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 457 through 460 removed outlier: 5.435A pdb=" N ARG B 458 " --> pdb=" O PHE B 448 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N PHE B 448 " --> pdb=" O ARG B 458 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 457 through 460 removed outlier: 5.435A pdb=" N ARG B 458 " --> pdb=" O PHE B 448 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N PHE B 448 " --> pdb=" O ARG B 458 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL B 446 " --> pdb=" O GLN B 495 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLN B 495 " --> pdb=" O VAL B 446 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 517 through 520 removed outlier: 6.611A pdb=" N LEU B 599 " --> pdb=" O LEU B 632 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL B 634 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N PHE B 601 " --> pdb=" O VAL B 634 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LYS B 469 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ILE B 648 " --> pdb=" O LYS B 469 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA B 471 " --> pdb=" O ILE B 648 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU B 650 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL B 473 " --> pdb=" O LEU B 650 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU B 657 " --> pdb=" O VAL B 649 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS B 651 " --> pdb=" O VAL B 655 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N VAL B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) 666 hydrogen bonds defined for protein. 1950 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: 3.23 Time building geometry restraints manager: 3.05 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: 2905 1.34 - 1.45: 1236 1.45 - 1.57: 5197 1.57 - 1.69: 10 1.69 - 1.80: 48 Bond restraints: 9396 Sorted by residual: bond pdb=" C4 ATP B 801 " pdb=" C5 ATP B 801 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.66e+01 bond pdb=" C4 ATP A 801 " pdb=" C5 ATP A 801 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.56e+01 bond pdb=" C5 ATP A 801 " pdb=" C6 ATP A 801 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.98e+01 bond pdb=" C5 ATP B 801 " pdb=" C6 ATP B 801 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.96e+01 bond pdb=" C5 ATP B 801 " pdb=" N7 ATP B 801 " ideal model delta sigma weight residual 1.387 1.339 0.048 1.00e-02 1.00e+04 2.33e+01 ... (remaining 9391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.44: 12676 4.44 - 8.89: 78 8.89 - 13.33: 0 13.33 - 17.77: 4 17.77 - 22.22: 2 Bond angle restraints: 12760 Sorted by residual: angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 117.65 22.22 1.00e+00 1.00e+00 4.94e+02 angle pdb=" PB ATP B 801 " pdb=" O3B ATP B 801 " pdb=" PG ATP B 801 " ideal model delta sigma weight residual 139.87 117.67 22.20 1.00e+00 1.00e+00 4.93e+02 angle pdb=" PA ATP B 801 " pdb=" O3A ATP B 801 " pdb=" PB ATP B 801 " ideal model delta sigma weight residual 136.83 120.00 16.83 1.00e+00 1.00e+00 2.83e+02 angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 120.02 16.81 1.00e+00 1.00e+00 2.82e+02 angle pdb=" C5 ATP A 801 " pdb=" C4 ATP A 801 " pdb=" N3 ATP A 801 " ideal model delta sigma weight residual 126.80 118.53 8.27 1.00e+00 1.00e+00 6.84e+01 ... (remaining 12755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 5105 17.30 - 34.60: 438 34.60 - 51.90: 69 51.90 - 69.19: 16 69.19 - 86.49: 22 Dihedral angle restraints: 5650 sinusoidal: 2248 harmonic: 3402 Sorted by residual: dihedral pdb=" CA ARG B 489 " pdb=" C ARG B 489 " pdb=" N SER B 490 " pdb=" CA SER B 490 " ideal model delta harmonic sigma weight residual 180.00 160.29 19.71 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ARG A 489 " pdb=" C ARG A 489 " pdb=" N SER A 490 " pdb=" CA SER A 490 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" N GLU A 412 " pdb=" C GLU A 412 " pdb=" CA GLU A 412 " pdb=" CB GLU A 412 " ideal model delta harmonic sigma weight residual 122.80 131.50 -8.70 0 2.50e+00 1.60e-01 1.21e+01 ... (remaining 5647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1159 0.057 - 0.113: 278 0.113 - 0.170: 39 0.170 - 0.226: 6 0.226 - 0.283: 4 Chirality restraints: 1486 Sorted by residual: chirality pdb=" CB ILE A 171 " pdb=" CA ILE A 171 " pdb=" CG1 ILE A 171 " pdb=" CG2 ILE A 171 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB ILE B 171 " pdb=" CA ILE B 171 " pdb=" CG1 ILE B 171 " pdb=" CG2 ILE B 171 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA GLU A 412 " pdb=" N GLU A 412 " pdb=" C GLU A 412 " pdb=" CB GLU A 412 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 1483 not shown) Planarity restraints: 1608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 427 " 0.053 5.00e-02 4.00e+02 7.78e-02 9.69e+00 pdb=" N PRO B 428 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 428 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 428 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 427 " 0.053 5.00e-02 4.00e+02 7.78e-02 9.68e+00 pdb=" N PRO A 428 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 428 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 428 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 596 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO A 597 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 597 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 597 " -0.021 5.00e-02 4.00e+02 ... (remaining 1605 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 110 2.62 - 3.19: 8434 3.19 - 3.76: 15330 3.76 - 4.33: 20456 4.33 - 4.90: 34298 Nonbonded interactions: 78628 Sorted by model distance: nonbonded pdb=" NE2 GLN B 522 " pdb="MG MG B 802 " model vdw 2.053 2.250 nonbonded pdb=" OD2 ASP A 207 " pdb=" OG1 THR A 423 " model vdw 2.215 3.040 nonbonded pdb=" OD2 ASP B 207 " pdb=" OG1 THR B 423 " model vdw 2.215 3.040 nonbonded pdb=" OG SER B 306 " pdb=" OE1 GLU B 322 " model vdw 2.229 3.040 nonbonded pdb=" OG SER A 306 " pdb=" OE1 GLU A 322 " model vdw 2.229 3.040 ... (remaining 78623 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.230 Find NCS groups from input model: 0.270 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: 0.010 Load rotamer database and sin/cos tables:11.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 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 : 0.007 0.082 9396 Z= 0.412 Angle : 0.951 22.218 12760 Z= 0.607 Chirality : 0.051 0.283 1486 Planarity : 0.005 0.078 1608 Dihedral : 14.353 86.493 3458 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: -0.18 (0.23), residues: 1170 helix: 0.36 (0.17), residues: 788 sheet: -1.18 (0.55), residues: 66 loop : -0.80 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 675 HIS 0.007 0.001 HIS A 132 PHE 0.013 0.002 PHE A 259 TYR 0.014 0.002 TYR A 274 ARG 0.009 0.001 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.101 Fit side-chains REVERT: A 190 LYS cc_start: 0.7544 (mttm) cc_final: 0.7213 (mtpm) REVERT: A 425 ARG cc_start: 0.8006 (ptp-110) cc_final: 0.7737 (ptp90) REVERT: B 190 LYS cc_start: 0.7544 (mttm) cc_final: 0.7204 (mtpm) REVERT: B 425 ARG cc_start: 0.8008 (ptp-110) cc_final: 0.7747 (ptp90) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 1.7071 time to fit residues: 207.3217 Evaluate side-chains 75 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.173 ------------------------------------------------------------------------------- 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: 1.9990 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 GLN A 552 GLN B 495 GLN B 552 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9396 Z= 0.241 Angle : 0.603 11.977 12760 Z= 0.312 Chirality : 0.043 0.160 1486 Planarity : 0.004 0.047 1608 Dihedral : 6.630 57.684 1348 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.34 % Allowed : 10.70 % Favored : 87.96 % 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: 0.85 (0.24), residues: 1170 helix: 1.25 (0.18), residues: 788 sheet: -1.37 (0.58), residues: 66 loop : -0.58 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 110 HIS 0.005 0.001 HIS A 557 PHE 0.010 0.001 PHE B 316 TYR 0.015 0.001 TYR A 642 ARG 0.003 0.000 ARG A 405 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 1.065 Fit side-chains REVERT: A 190 LYS cc_start: 0.7446 (mttm) cc_final: 0.7144 (mtpm) REVERT: A 248 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.8012 (mp) REVERT: A 289 ARG cc_start: 0.6927 (ttp80) cc_final: 0.6585 (ttp-110) REVERT: B 190 LYS cc_start: 0.7433 (mttm) cc_final: 0.7127 (mtpm) REVERT: B 248 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.8034 (mp) REVERT: B 289 ARG cc_start: 0.6968 (ttp80) cc_final: 0.6630 (ttp-110) outliers start: 13 outliers final: 8 residues processed: 93 average time/residue: 1.2677 time to fit residues: 126.6180 Evaluate side-chains 79 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 552 GLN Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 562 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9396 Z= 0.236 Angle : 0.579 10.830 12760 Z= 0.295 Chirality : 0.042 0.154 1486 Planarity : 0.003 0.037 1608 Dihedral : 6.439 58.228 1348 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.47 % Allowed : 11.93 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.25), residues: 1170 helix: 1.59 (0.18), residues: 788 sheet: -1.34 (0.59), residues: 66 loop : -0.50 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 110 HIS 0.005 0.001 HIS A 557 PHE 0.010 0.001 PHE A 316 TYR 0.016 0.001 TYR A 642 ARG 0.004 0.000 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 78 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: A 190 LYS cc_start: 0.7402 (mttm) cc_final: 0.7109 (mtpm) REVERT: A 248 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7976 (mp) REVERT: A 289 ARG cc_start: 0.6848 (ttp80) cc_final: 0.6620 (ttp-110) REVERT: B 190 LYS cc_start: 0.7438 (mttm) cc_final: 0.7129 (mtpm) REVERT: B 289 ARG cc_start: 0.6869 (ttp80) cc_final: 0.6632 (ttp-110) outliers start: 24 outliers final: 5 residues processed: 93 average time/residue: 1.3133 time to fit residues: 131.0253 Evaluate side-chains 74 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 105 optimal weight: 0.4980 chunk 112 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9396 Z= 0.268 Angle : 0.592 12.329 12760 Z= 0.299 Chirality : 0.043 0.169 1486 Planarity : 0.003 0.033 1608 Dihedral : 6.540 59.980 1348 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.29 % Allowed : 12.24 % Favored : 84.47 % 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: 1.41 (0.25), residues: 1170 helix: 1.75 (0.18), residues: 788 sheet: -1.51 (0.58), residues: 66 loop : -0.51 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 261 HIS 0.003 0.001 HIS B 661 PHE 0.011 0.001 PHE A 316 TYR 0.017 0.001 TYR A 642 ARG 0.004 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 76 time to evaluate : 1.177 Fit side-chains REVERT: A 190 LYS cc_start: 0.7481 (mttm) cc_final: 0.7178 (mtpm) REVERT: A 289 ARG cc_start: 0.6844 (ttp80) cc_final: 0.6545 (ttp-110) REVERT: A 673 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7611 (mt-10) REVERT: B 190 LYS cc_start: 0.7449 (mttm) cc_final: 0.7143 (mtpm) REVERT: B 289 ARG cc_start: 0.6841 (ttp80) cc_final: 0.6545 (ttp-110) REVERT: B 673 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7552 (mt-10) outliers start: 32 outliers final: 14 residues processed: 97 average time/residue: 1.1751 time to fit residues: 123.1433 Evaluate side-chains 86 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 70 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 673 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 0.0980 chunk 95 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 100 optimal weight: 0.6980 chunk 28 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9396 Z= 0.191 Angle : 0.565 11.052 12760 Z= 0.285 Chirality : 0.041 0.165 1486 Planarity : 0.003 0.042 1608 Dihedral : 6.245 56.086 1348 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.88 % Allowed : 13.89 % Favored : 83.23 % 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: 1.63 (0.25), residues: 1170 helix: 1.92 (0.18), residues: 788 sheet: -1.39 (0.58), residues: 66 loop : -0.46 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 364 HIS 0.003 0.001 HIS A 211 PHE 0.012 0.001 PHE B 396 TYR 0.018 0.001 TYR A 642 ARG 0.011 0.000 ARG B 662 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 79 time to evaluate : 1.087 Fit side-chains revert: symmetry clash REVERT: A 289 ARG cc_start: 0.6722 (ttp80) cc_final: 0.6483 (ttp-110) REVERT: A 673 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7584 (mt-10) REVERT: B 190 LYS cc_start: 0.7424 (mttm) cc_final: 0.7103 (mtpm) REVERT: B 289 ARG cc_start: 0.6744 (ttp80) cc_final: 0.6504 (ttp-110) REVERT: B 673 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7550 (mt-10) outliers start: 28 outliers final: 16 residues processed: 96 average time/residue: 1.2170 time to fit residues: 126.3545 Evaluate side-chains 88 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 70 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 614 GLN Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 673 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 58 optimal weight: 10.0000 chunk 108 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1881 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: