Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 03:28:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uac_26420/04_2023/7uac_26420.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uac_26420/04_2023/7uac_26420.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uac_26420/04_2023/7uac_26420.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uac_26420/04_2023/7uac_26420.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uac_26420/04_2023/7uac_26420.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uac_26420/04_2023/7uac_26420.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 0.045 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 Ca 2 9.91 5 Zn 1 6.06 5 S 21 5.16 5 C 2860 2.51 5 N 759 2.21 5 O 897 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 39": "OE1" <-> "OE2" Residue "H GLU 45": "OE1" <-> "OE2" Residue "H GLU 100": "OE1" <-> "OE2" Residue "H GLU 114": "OE1" <-> "OE2" Residue "H GLU 116": "OE1" <-> "OE2" Residue "H GLU 131": "OE1" <-> "OE2" Residue "H GLU 154": "OE1" <-> "OE2" Residue "H GLU 156": "OE1" <-> "OE2" Residue "H TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 234": "OE1" <-> "OE2" Residue "H GLU 272": "OE1" <-> "OE2" Residue "H GLU 299": "OE1" <-> "OE2" Residue "H GLU 325": "OE1" <-> "OE2" Residue "H GLU 326": "OE1" <-> "OE2" Residue "H GLU 331": "OE1" <-> "OE2" Residue "H ARG 372": "NH1" <-> "NH2" Residue "H GLU 397": "OE1" <-> "OE2" Residue "H GLU 398": "OE1" <-> "OE2" Residue "H GLU 446": "OE1" <-> "OE2" Residue "H GLU 492": "OE1" <-> "OE2" Residue "H GLU 498": "OE1" <-> "OE2" Residue "H ASP 512": "OD1" <-> "OD2" Residue "H GLU 514": "OE1" <-> "OE2" Residue "H GLU 594": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 4540 Number of models: 1 Model: "" Number of chains: 6 Chain: "H" Number of atoms: 4404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4404 Classifications: {'peptide': 546} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 528} Chain breaks: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.92, per 1000 atoms: 0.64 Number of scatterers: 4540 At special positions: 0 Unit cell: (94.34, 77.38, 92.22, 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) Zn 1 29.99 Ca 2 19.99 S 21 16.00 O 897 8.00 N 759 7.00 C 2860 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 107 " - pdb=" SG CYS H 259 " distance=2.03 Simple disulfide: pdb=" SG CYS H 128 " - pdb=" SG CYS H 147 " distance=2.02 Simple disulfide: pdb=" SG CYS H 269 " - pdb=" SG CYS H 277 " distance=2.03 Simple disulfide: pdb=" SG CYS H 343 " - pdb=" SG CYS H 431 " distance=2.05 Simple disulfide: pdb=" SG CYS H 557 " - pdb=" SG CYS H 559 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " BETA1-6 " NAG C 1 " - " FUC C 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 1 " - " ASN H 140 " " NAG B 1 " - " ASN H 222 " " NAG C 1 " - " ASN H 414 " " NAG D 1 " - " ASN H 440 " Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 619.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 702 " pdb="ZN ZN H 702 " - pdb=" NE2 HIS H 159 " pdb="ZN ZN H 702 " - pdb=" NE2 HIS H 165 " pdb="ZN ZN H 702 " - pdb=" NE2 HIS H 155 " 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1016 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 9 sheets defined 21.8% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'H' and resid 42 through 51 Processing helix chain 'H' and resid 88 through 106 Processing helix chain 'H' and resid 149 through 161 Processing helix chain 'H' and resid 165 through 169 removed outlier: 3.606A pdb=" N SER H 168 " --> pdb=" O HIS H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 174 Processing helix chain 'H' and resid 180 through 183 Processing helix chain 'H' and resid 187 through 192 Processing helix chain 'H' and resid 232 through 238 Processing helix chain 'H' and resid 246 through 258 Processing helix chain 'H' and resid 275 through 279 Processing helix chain 'H' and resid 440 through 448 Processing helix chain 'H' and resid 516 through 520 Processing helix chain 'H' and resid 546 through 550 Processing helix chain 'H' and resid 573 through 577 Processing helix chain 'H' and resid 582 through 586 Processing helix chain 'H' and resid 597 through 600 Processing sheet with id=AA1, first strand: chain 'H' and resid 110 through 112 removed outlier: 7.939A pdb=" N PHE H 122 " --> pdb=" O PRO H 80 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE H 82 " --> pdb=" O PHE H 122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 176 through 178 Processing sheet with id=AA3, first strand: chain 'H' and resid 265 through 269 Processing sheet with id=AA4, first strand: chain 'H' and resid 265 through 269 removed outlier: 5.664A pdb=" N LEU H 421 " --> pdb=" O LYS H 349 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LYS H 349 " --> pdb=" O LEU H 421 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ASP H 423 " --> pdb=" O PHE H 347 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE H 347 " --> pdb=" O ASP H 423 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 280 through 281 removed outlier: 6.826A pdb=" N LEU H 358 " --> pdb=" O THR H 379 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR H 379 " --> pdb=" O LEU H 358 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL H 360 " --> pdb=" O VAL H 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 434 through 438 Processing sheet with id=AA7, first strand: chain 'H' and resid 454 through 455 Processing sheet with id=AA8, first strand: chain 'H' and resid 454 through 455 removed outlier: 3.961A pdb=" N GLY H 466 " --> pdb=" O CYS H 489 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU H 482 " --> pdb=" O GLY H 569 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU H 484 " --> pdb=" O TRP H 567 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 551 through 554 156 hydrogen bonds defined for protein. 375 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.28 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: 1.20 - 1.32: 861 1.32 - 1.45: 1258 1.45 - 1.57: 2495 1.57 - 1.69: 0 1.69 - 1.82: 30 Bond restraints: 4644 Sorted by residual: bond pdb=" N PRO H 412 " pdb=" CA PRO H 412 " ideal model delta sigma weight residual 1.471 1.410 0.061 1.29e-02 6.01e+03 2.26e+01 bond pdb=" C GLN H 40 " pdb=" N LYS H 41 " ideal model delta sigma weight residual 1.331 1.403 -0.072 1.51e-02 4.39e+03 2.26e+01 bond pdb=" C GLU H 39 " pdb=" N GLN H 40 " ideal model delta sigma weight residual 1.330 1.385 -0.055 1.32e-02 5.74e+03 1.75e+01 bond pdb=" N ILE H 276 " pdb=" CA ILE H 276 " ideal model delta sigma weight residual 1.459 1.506 -0.047 1.25e-02 6.40e+03 1.43e+01 bond pdb=" CA SER H 168 " pdb=" CB SER H 168 " ideal model delta sigma weight residual 1.530 1.472 0.058 1.54e-02 4.22e+03 1.40e+01 ... (remaining 4639 not shown) Histogram of bond angle deviations from ideal: 98.46 - 105.72: 97 105.72 - 112.99: 2201 112.99 - 120.25: 2162 120.25 - 127.52: 1783 127.52 - 134.78: 49 Bond angle restraints: 6292 Sorted by residual: angle pdb=" CA PHE H 590 " pdb=" CB PHE H 590 " pdb=" CG PHE H 590 " ideal model delta sigma weight residual 113.80 120.35 -6.55 1.00e+00 1.00e+00 4.28e+01 angle pdb=" N GLN H 135 " pdb=" CA GLN H 135 " pdb=" C GLN H 135 " ideal model delta sigma weight residual 113.30 104.70 8.60 1.34e+00 5.57e-01 4.12e+01 angle pdb=" C PRO H 412 " pdb=" CA PRO H 412 " pdb=" CB PRO H 412 " ideal model delta sigma weight residual 112.55 121.90 -9.35 1.50e+00 4.44e-01 3.88e+01 angle pdb=" CA GLY H 138 " pdb=" C GLY H 138 " pdb=" O GLY H 138 " ideal model delta sigma weight residual 122.23 118.25 3.98 6.90e-01 2.10e+00 3.32e+01 angle pdb=" CA ASP H 134 " pdb=" CB ASP H 134 " pdb=" CG ASP H 134 " ideal model delta sigma weight residual 112.60 118.31 -5.71 1.00e+00 1.00e+00 3.26e+01 ... (remaining 6287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 2460 17.97 - 35.94: 159 35.94 - 53.91: 26 53.91 - 71.88: 8 71.88 - 89.85: 3 Dihedral angle restraints: 2656 sinusoidal: 1075 harmonic: 1581 Sorted by residual: dihedral pdb=" CB CYS H 128 " pdb=" SG CYS H 128 " pdb=" SG CYS H 147 " pdb=" CB CYS H 147 " ideal model delta sinusoidal sigma weight residual 93.00 151.89 -58.89 1 1.00e+01 1.00e-02 4.64e+01 dihedral pdb=" C PRO H 412 " pdb=" N PRO H 412 " pdb=" CA PRO H 412 " pdb=" CB PRO H 412 " ideal model delta harmonic sigma weight residual -120.70 -134.70 14.00 0 2.50e+00 1.60e-01 3.14e+01 dihedral pdb=" CA ILE H 424 " pdb=" C ILE H 424 " pdb=" N THR H 425 " pdb=" CA THR H 425 " ideal model delta harmonic sigma weight residual 180.00 153.34 26.66 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 2653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 571 0.128 - 0.256: 109 0.256 - 0.384: 18 0.384 - 0.511: 2 0.511 - 0.639: 1 Chirality restraints: 701 Sorted by residual: chirality pdb=" C1 FUC C 4 " pdb=" O6 NAG C 1 " pdb=" C2 FUC C 4 " pdb=" O5 FUC C 4 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.54e+02 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 7.76e+01 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 5.09e+01 ... (remaining 698 not shown) Planarity restraints: 809 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " -0.228 2.00e-02 2.50e+03 1.93e-01 4.64e+02 pdb=" C7 NAG A 1 " 0.056 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " -0.155 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " 0.326 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.218 2.00e-02 2.50e+03 1.82e-01 4.12e+02 pdb=" C7 NAG D 1 " 0.059 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.154 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.300 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " 0.115 2.00e-02 2.50e+03 9.51e-02 1.13e+02 pdb=" C7 NAG C 1 " -0.033 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " 0.087 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " -0.151 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " -0.018 2.00e-02 2.50e+03 ... (remaining 806 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.28: 3 2.28 - 2.94: 1967 2.94 - 3.59: 5970 3.59 - 4.25: 11163 4.25 - 4.90: 18169 Nonbonded interactions: 37272 Sorted by model distance: nonbonded pdb=" OD1 ASP H 58 " pdb="ZN ZN H 702 " model vdw 1.626 2.230 nonbonded pdb=" CG ASP H 58 " pdb="ZN ZN H 702 " model vdw 2.169 2.460 nonbonded pdb=" OD2 ASP H 58 " pdb="ZN ZN H 702 " model vdw 2.250 2.230 nonbonded pdb=" OD1 ASP H 288 " pdb="CA CA H 701 " model vdw 2.332 2.510 nonbonded pdb=" OD1 ASP H 285 " pdb="CA CA H 701 " model vdw 2.343 2.510 ... (remaining 37267 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' } 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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.630 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 17.480 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 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 : 0.012 0.072 4644 Z= 0.766 Angle : 1.786 9.345 6292 Z= 1.201 Chirality : 0.109 0.639 701 Planarity : 0.015 0.193 805 Dihedral : 12.813 89.846 1625 Min Nonbonded Distance : 1.626 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.98 % Peptide Plane: Cis-proline : 11.76 % 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: -0.63 (0.33), residues: 538 helix: -0.90 (0.48), residues: 78 sheet: 0.08 (0.43), residues: 127 loop : -0.44 (0.32), residues: 333 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.546 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 1.2767 time to fit residues: 214.8743 Evaluate side-chains 95 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.535 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 16 optimal weight: 0.0980 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 40 GLN H 124 GLN H 203 ASN H 370 ASN H 386 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3042 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: