Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 03:22:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uae_26422/04_2023/7uae_26422.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uae_26422/04_2023/7uae_26422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uae_26422/04_2023/7uae_26422.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uae_26422/04_2023/7uae_26422.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uae_26422/04_2023/7uae_26422.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uae_26422/04_2023/7uae_26422.pdb" } resolution = 2.6 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= 0.044 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 2834 2.51 5 N 748 2.21 5 O 907 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A GLU 331": "OE1" <-> "OE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A ARG 458": "NH1" <-> "NH2" Residue "A ARG 483": "NH1" <-> "NH2" Residue "A ARG 504": "NH1" <-> "NH2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "A ARG 546": "NH1" <-> "NH2" Residue "A ARG 549": "NH1" <-> "NH2" Residue "A ARG 578": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 4513 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4313 Classifications: {'peptide': 535} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 515} 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: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: "E" 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: "F" 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: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 17 Unusual residues: {' CA': 2, ' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.80, per 1000 atoms: 0.62 Number of scatterers: 4513 At special positions: 0 Unit cell: (99.64, 81.62, 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 907 8.00 N 748 7.00 C 2834 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 259 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 431 " distance=2.04 Simple disulfide: pdb=" SG CYS A 557 " - pdb=" SG CYS A 559 " distance=2.05 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 B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " BETA1-6 " NAG F 1 " - " FUC F 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 704 " - " ASN A 539 " " NAG B 1 " - " ASN A 140 " " NAG C 1 " - " ASN A 258 " " NAG D 1 " - " ASN A 222 " " NAG E 1 " - " ASN A 440 " " NAG F 1 " - " ASN A 414 " Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 651.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 702 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 165 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 155 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 159 " 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 998 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 10 sheets defined 23.6% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 88 through 106 Processing helix chain 'A' and resid 149 through 162 Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 171 through 174 Processing helix chain 'A' and resid 180 through 183 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 232 through 238 Processing helix chain 'A' and resid 246 through 258 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 440 through 448 removed outlier: 4.317A pdb=" N GLU A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 516 through 520 Processing helix chain 'A' and resid 535 through 539 Processing helix chain 'A' and resid 546 through 551 Processing helix chain 'A' and resid 573 through 577 Processing helix chain 'A' and resid 597 through 600 Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 112 removed outlier: 7.977A pdb=" N PHE A 122 " --> pdb=" O PRO A 80 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE A 82 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE A 121 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 178 Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 269 Processing sheet with id=AA5, first strand: chain 'A' and resid 265 through 269 removed outlier: 5.726A pdb=" N LEU A 421 " --> pdb=" O LYS A 349 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LYS A 349 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ASP A 423 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE A 347 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 280 through 281 removed outlier: 6.790A pdb=" N LEU A 358 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N THR A 379 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL A 360 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 434 through 438 Processing sheet with id=AA8, first strand: chain 'A' and resid 454 through 455 Processing sheet with id=AA9, first strand: chain 'A' and resid 454 through 455 removed outlier: 3.951A pdb=" N GLY A 466 " --> pdb=" O CYS A 489 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU A 482 " --> pdb=" O GLY A 569 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 552 through 553 158 hydrogen bonds defined for protein. 354 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: 1.36 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1084 1.33 - 1.45: 1057 1.45 - 1.57: 2449 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 4620 Sorted by residual: bond pdb=" CZ ARG A 169 " pdb=" NH2 ARG A 169 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 1.01e+01 bond pdb=" CZ ARG A 172 " pdb=" NH2 ARG A 172 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.92e+00 bond pdb=" N VAL A 371 " pdb=" CA VAL A 371 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.71e+00 bond pdb=" CZ ARG A 518 " pdb=" NH2 ARG A 518 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.58e+00 bond pdb=" CZ ARG A 103 " pdb=" NH2 ARG A 103 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.47e+00 ... (remaining 4615 not shown) Histogram of bond angle deviations from ideal: 97.33 - 104.87: 70 104.87 - 112.40: 2083 112.40 - 119.94: 1989 119.94 - 127.47: 2086 127.47 - 135.01: 43 Bond angle restraints: 6271 Sorted by residual: angle pdb=" CA PHE A 590 " pdb=" CB PHE A 590 " pdb=" CG PHE A 590 " ideal model delta sigma weight residual 113.80 118.92 -5.12 1.00e+00 1.00e+00 2.62e+01 angle pdb=" CA ASP A 564 " pdb=" CB ASP A 564 " pdb=" CG ASP A 564 " ideal model delta sigma weight residual 112.60 117.67 -5.07 1.00e+00 1.00e+00 2.57e+01 angle pdb=" N TYR A 113 " pdb=" CA TYR A 113 " pdb=" C TYR A 113 " ideal model delta sigma weight residual 111.07 116.26 -5.19 1.07e+00 8.73e-01 2.35e+01 angle pdb=" CB HIS A 573 " pdb=" CG HIS A 573 " pdb=" CD2 HIS A 573 " ideal model delta sigma weight residual 131.20 124.97 6.23 1.30e+00 5.92e-01 2.30e+01 angle pdb=" OE1 GLN A 345 " pdb=" CD GLN A 345 " pdb=" NE2 GLN A 345 " ideal model delta sigma weight residual 122.60 117.87 4.73 1.00e+00 1.00e+00 2.23e+01 ... (remaining 6266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 2422 18.01 - 36.03: 148 36.03 - 54.04: 23 54.04 - 72.05: 14 72.05 - 90.06: 2 Dihedral angle restraints: 2609 sinusoidal: 1054 harmonic: 1555 Sorted by residual: dihedral pdb=" CB CYS A 128 " pdb=" SG CYS A 128 " pdb=" SG CYS A 147 " pdb=" CB CYS A 147 " ideal model delta sinusoidal sigma weight residual 93.00 -176.94 -90.06 1 1.00e+01 1.00e-02 9.61e+01 dihedral pdb=" CB CYS A 557 " pdb=" SG CYS A 557 " pdb=" SG CYS A 559 " pdb=" CB CYS A 559 " ideal model delta sinusoidal sigma weight residual -86.00 -139.17 53.17 1 1.00e+01 1.00e-02 3.84e+01 dihedral pdb=" CA TRP A 567 " pdb=" C TRP A 567 " pdb=" N SER A 568 " pdb=" CA SER A 568 " ideal model delta harmonic sigma weight residual 180.00 150.29 29.71 0 5.00e+00 4.00e-02 3.53e+01 ... (remaining 2606 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 398 0.079 - 0.157: 236 0.157 - 0.236: 62 0.236 - 0.314: 14 0.314 - 0.393: 4 Chirality restraints: 714 Sorted by residual: 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 -2.12 -0.28 2.00e-02 2.50e+03 1.93e+02 chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.44e+01 chirality pdb=" C1 FUC F 4 " pdb=" O6 NAG F 1 " pdb=" C2 FUC F 4 " pdb=" O5 FUC F 4 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.73e+01 ... (remaining 711 not shown) Planarity restraints: 803 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " -0.314 2.00e-02 2.50e+03 2.72e-01 9.25e+02 pdb=" C7 NAG C 1 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " -0.027 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " 0.474 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " -0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.205 2.00e-02 2.50e+03 1.68e-01 3.55e+02 pdb=" C7 NAG D 1 " 0.056 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.148 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.273 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 704 " 0.183 2.00e-02 2.50e+03 1.51e-01 2.85e+02 pdb=" C7 NAG A 704 " -0.051 2.00e-02 2.50e+03 pdb=" C8 NAG A 704 " 0.134 2.00e-02 2.50e+03 pdb=" N2 NAG A 704 " -0.245 2.00e-02 2.50e+03 pdb=" O7 NAG A 704 " -0.021 2.00e-02 2.50e+03 ... (remaining 800 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 823 2.81 - 3.33: 4208 3.33 - 3.85: 7306 3.85 - 4.38: 9238 4.38 - 4.90: 15059 Nonbonded interactions: 36634 Sorted by model distance: nonbonded pdb=" OD1 ASP A 288 " pdb="CA CA A 701 " model vdw 2.282 2.510 nonbonded pdb=" OE2 GLU A 272 " pdb="CA CA A 703 " model vdw 2.302 2.510 nonbonded pdb=" O TYR A 313 " pdb="CA CA A 703 " model vdw 2.329 2.510 nonbonded pdb=" OD1 ASP A 285 " pdb="CA CA A 701 " model vdw 2.329 2.510 nonbonded pdb=" OD2 ASP A 285 " pdb="CA CA A 701 " model vdw 2.379 2.510 ... (remaining 36629 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 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' } 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: 0.000 Extract box with map and model: 2.660 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 17.440 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 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 0.041 4620 Z= 0.754 Angle : 1.756 9.028 6271 Z= 1.171 Chirality : 0.102 0.393 714 Planarity : 0.020 0.272 797 Dihedral : 12.757 82.604 1596 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 0.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 10.53 % 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 (0.34), residues: 533 helix: -0.97 (0.58), residues: 62 sheet: 0.51 (0.43), residues: 131 loop : -0.13 (0.33), residues: 340 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.539 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 1.2334 time to fit residues: 150.7437 Evaluate side-chains 76 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.561 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 461 ASN A 474 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 4620 Z= 0.234 Angle : 0.651 9.172 6271 Z= 0.343 Chirality : 0.045 0.197 714 Planarity : 0.004 0.026 797 Dihedral : 6.018 27.256 585 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.01 (0.34), residues: 533 helix: -0.23 (0.61), residues: 69 sheet: 0.45 (0.43), residues: 137 loop : -0.04 (0.33), residues: 327 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.569 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 84 average time/residue: 1.1235 time to fit residues: 98.3800 Evaluate side-chains 79 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 0.557 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.8257 time to fit residues: 2.4533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 4620 Z= 0.215 Angle : 0.575 9.490 6271 Z= 0.305 Chirality : 0.044 0.198 714 Planarity : 0.003 0.029 797 Dihedral : 5.261 25.997 585 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 3.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 (0.36), residues: 533 helix: 0.17 (0.64), residues: 69 sheet: 0.42 (0.43), residues: 140 loop : 0.07 (0.34), residues: 324 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 73 time to evaluate : 0.584 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 80 average time/residue: 1.1306 time to fit residues: 94.2662 Evaluate side-chains 75 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.547 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.0436 time to fit residues: 0.8875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 0.2980 chunk 36 optimal weight: 0.0050 chunk 25 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 HIS ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 4620 Z= 0.162 Angle : 0.551 10.123 6271 Z= 0.288 Chirality : 0.043 0.212 714 Planarity : 0.003 0.029 797 Dihedral : 4.968 24.249 585 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer Outliers : 2.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.23 (0.36), residues: 533 helix: 0.59 (0.65), residues: 66 sheet: 0.42 (0.43), residues: 148 loop : 0.02 (0.34), residues: 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.532 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 77 average time/residue: 0.9889 time to fit residues: 79.5424 Evaluate side-chains 75 residues out of total 477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.419 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.0363 time to fit residues: 0.6048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: