Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 03:21:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el7_28223/04_2023/8el7_28223_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el7_28223/04_2023/8el7_28223.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el7_28223/04_2023/8el7_28223.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el7_28223/04_2023/8el7_28223.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el7_28223/04_2023/8el7_28223_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el7_28223/04_2023/8el7_28223_updated.pdb" } resolution = 2.8 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= -0.001 sd= 0.198 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 27 5.16 5 C 2921 2.51 5 N 802 2.21 5 O 810 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 3": "OE1" <-> "OE2" Residue "B GLU 223": "OE1" <-> "OE2" 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: 4562 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1134 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 146, 1118 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain breaks: 5 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 87 Conformer: "B" Number of residues, atoms: 146, 1118 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain breaks: 5 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 87 bond proxies already assigned to first conformer: 1130 Conformer: "C" Number of residues, atoms: 146, 1118 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain breaks: 5 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 87 bond proxies already assigned to first conformer: 1130 Chain: "B" Number of atoms: 3428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3428 Classifications: {'peptide': 458, 'water': 5} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 15, 'TRANS': 442, None: 5} Not linked: pdbres="GLU B 494 " pdbres="HOH B 601 " Not linked: pdbres="HOH B 601 " pdbres="HOH B 602 " Not linked: pdbres="HOH B 602 " pdbres="HOH B 603 " Not linked: pdbres="HOH B 603 " pdbres="HOH B 604 " Not linked: pdbres="HOH B 604 " pdbres="HOH B 605 " Chain breaks: 2 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 282 Unresolved non-hydrogen dihedrals: 188 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'TPO:plan-1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 15, 'GLU:plan': 19, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 171 Time building chain proxies: 4.29, per 1000 atoms: 0.94 Number of scatterers: 4562 At special positions: 0 Unit cell: (54.5344, 80.0974, 110.773, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 2 15.00 O 810 8.00 N 802 7.00 C 2921 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.99 Conformation dependent library (CDL) restraints added in 1.2 seconds 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1168 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 2 sheets defined 58.8% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 252 through 263 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 299 through 303 Processing helix chain 'A' and resid 318 through 336 removed outlier: 3.676A pdb=" N PHE A 331 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 375 Processing helix chain 'B' and resid 4 through 10 Processing helix chain 'B' and resid 15 through 28 removed outlier: 3.819A pdb=" N GLU B 19 " --> pdb=" O ALA B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 55 removed outlier: 3.896A pdb=" N GLU B 40 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ASP B 41 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS B 45 " --> pdb=" O LYS B 42 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE B 51 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 55 " --> pdb=" O LYS B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 75 removed outlier: 4.059A pdb=" N ARG B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 95 Processing helix chain 'B' and resid 111 through 127 Processing helix chain 'B' and resid 130 through 138 Processing helix chain 'B' and resid 140 through 150 Processing helix chain 'B' and resid 158 through 174 Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 188 through 200 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.535A pdb=" N ASN B 236 " --> pdb=" O LYS B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 265 removed outlier: 3.513A pdb=" N SER B 250 " --> pdb=" O GLU B 247 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N HIS B 251 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 255 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N MET B 256 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 287 removed outlier: 4.100A pdb=" N ASN B 287 " --> pdb=" O ASN B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 296 removed outlier: 4.747A pdb=" N ASP B 294 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL B 295 " --> pdb=" O CYS B 292 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 296 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 354 Processing helix chain 'B' and resid 360 through 376 removed outlier: 4.050A pdb=" N THR B 364 " --> pdb=" O ARG B 360 " (cutoff:3.500A) Proline residue: B 365 - end of helix removed outlier: 3.579A pdb=" N ALA B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 388 removed outlier: 3.840A pdb=" N ASP B 386 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN B 387 " --> pdb=" O PHE B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 414 removed outlier: 3.697A pdb=" N MET B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR B 414 " --> pdb=" O VAL B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 432 removed outlier: 3.634A pdb=" N LEU B 428 " --> pdb=" O ALA B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 442 removed outlier: 3.639A pdb=" N TYR B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 455 Processing helix chain 'B' and resid 476 through 484 Proline residue: B 483 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 42 through 44 Processing sheet with id= B, first strand: chain 'A' and resid 229 through 235 removed outlier: 6.857A pdb=" N SER A 272 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N PHE A 232 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE A 274 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N VAL A 234 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE A 276 " --> pdb=" O VAL A 234 " (cutoff:3.500A) 215 hydrogen bonds defined for protein. 566 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: 1.11 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 728 1.31 - 1.44: 1153 1.44 - 1.56: 2711 1.56 - 1.68: 2 1.68 - 1.81: 38 Bond restraints: 4632 Sorted by residual: bond pdb=" O3P SEP B 468 " pdb=" P SEP B 468 " ideal model delta sigma weight residual 1.610 1.477 0.133 2.00e-02 2.50e+03 4.44e+01 bond pdb=" C ARG A 375 " pdb=" CA BARG A 375 " ideal model delta sigma weight residual 1.522 1.430 0.091 1.40e-02 5.10e+03 4.26e+01 bond pdb=" C ARG A 375 " pdb=" CA CARG A 375 " ideal model delta sigma weight residual 1.522 1.430 0.091 1.40e-02 5.10e+03 4.26e+01 bond pdb=" O1P SEP B 468 " pdb=" P SEP B 468 " ideal model delta sigma weight residual 1.610 1.480 0.130 2.00e-02 2.50e+03 4.22e+01 bond pdb=" O2P SEP B 468 " pdb=" P SEP B 468 " ideal model delta sigma weight residual 1.610 1.481 0.129 2.00e-02 2.50e+03 4.16e+01 ... (remaining 4627 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.88: 123 106.88 - 113.66: 2658 113.66 - 120.44: 1740 120.44 - 127.21: 1735 127.21 - 133.99: 39 Bond angle restraints: 6295 Sorted by residual: angle pdb=" N GLU B 4 " pdb=" CA GLU B 4 " pdb=" C GLU B 4 " ideal model delta sigma weight residual 111.28 115.77 -4.49 1.09e+00 8.42e-01 1.70e+01 angle pdb=" C TRP B 466 " pdb=" N TYR B 467 " pdb=" CA TYR B 467 " ideal model delta sigma weight residual 121.70 114.71 6.99 1.80e+00 3.09e-01 1.51e+01 angle pdb=" CA TRP B 466 " pdb=" C TRP B 466 " pdb=" N TYR B 467 " ideal model delta sigma weight residual 116.02 121.32 -5.30 1.42e+00 4.96e-01 1.39e+01 angle pdb=" N ALA B 15 " pdb=" CA ALA B 15 " pdb=" C ALA B 15 " ideal model delta sigma weight residual 113.38 117.91 -4.53 1.23e+00 6.61e-01 1.35e+01 angle pdb=" N GLY B 13 " pdb=" CA GLY B 13 " pdb=" C GLY B 13 " ideal model delta sigma weight residual 112.73 116.85 -4.12 1.20e+00 6.94e-01 1.18e+01 ... (remaining 6290 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 2582 17.32 - 34.64: 188 34.64 - 51.96: 31 51.96 - 69.28: 6 69.28 - 86.60: 5 Dihedral angle restraints: 2812 sinusoidal: 1029 harmonic: 1783 Sorted by residual: dihedral pdb=" CA GLY B 13 " pdb=" C GLY B 13 " pdb=" N GLU B 14 " pdb=" CA GLU B 14 " ideal model delta harmonic sigma weight residual 180.00 -155.43 -24.57 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" C TPO B 473 " pdb=" N TPO B 473 " pdb=" CA TPO B 473 " pdb=" CB TPO B 473 " ideal model delta harmonic sigma weight residual -122.60 -113.38 -9.22 0 2.50e+00 1.60e-01 1.36e+01 dihedral pdb=" N TRP B 466 " pdb=" C TRP B 466 " pdb=" CA TRP B 466 " pdb=" CB TRP B 466 " ideal model delta harmonic sigma weight residual 122.80 114.49 8.31 0 2.50e+00 1.60e-01 1.10e+01 ... (remaining 2809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 541 0.038 - 0.077: 177 0.077 - 0.115: 39 0.115 - 0.154: 10 0.154 - 0.192: 4 Chirality restraints: 771 Sorted by residual: chirality pdb=" CA ALA B 15 " pdb=" N ALA B 15 " pdb=" C ALA B 15 " pdb=" CB ALA B 15 " both_signs ideal model delta sigma weight residual False 2.48 2.29 0.19 2.00e-01 2.50e+01 9.25e-01 chirality pdb=" CA BARG A 375 " pdb=" N ARG A 375 " pdb=" C ARG A 375 " pdb=" CB BARG A 375 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.05e-01 chirality pdb=" CA CARG A 375 " pdb=" N ARG A 375 " pdb=" C ARG A 375 " pdb=" CB CARG A 375 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.05e-01 ... (remaining 768 not shown) Planarity restraints: 789 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 463 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.92e+00 pdb=" C GLY B 463 " -0.049 2.00e-02 2.50e+03 pdb=" O GLY B 463 " 0.019 2.00e-02 2.50e+03 pdb=" N ASP B 464 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 5 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.88e+00 pdb=" C ARG B 5 " -0.024 2.00e-02 2.50e+03 pdb=" O ARG B 5 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA B 6 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 478 " -0.006 2.00e-02 2.50e+03 1.18e-02 1.40e+00 pdb=" C TYR B 478 " 0.020 2.00e-02 2.50e+03 pdb=" O TYR B 478 " -0.008 2.00e-02 2.50e+03 pdb=" N LYS B 479 " -0.007 2.00e-02 2.50e+03 ... (remaining 786 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 1224 2.82 - 3.34: 4059 3.34 - 3.86: 6752 3.86 - 4.38: 7778 4.38 - 4.90: 14119 Nonbonded interactions: 33932 Sorted by model distance: nonbonded pdb=" O LEU B 80 " pdb=" OG1 THR B 84 " model vdw 2.295 2.440 nonbonded pdb=" O LEU B 70 " pdb=" OG SER B 74 " model vdw 2.311 2.440 nonbonded pdb=" N GLU B 3 " pdb=" OE1 GLU B 3 " model vdw 2.356 2.520 nonbonded pdb=" O PRO B 399 " pdb=" ND2 ASN B 407 " model vdw 2.374 2.520 nonbonded pdb=" N ASP B 464 " pdb=" OD1 ASP B 464 " model vdw 2.407 2.520 ... (remaining 33927 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.25 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: 0.690 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: 3.660 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.620 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.133 4632 Z= 0.418 Angle : 0.611 7.578 6295 Z= 0.356 Chirality : 0.042 0.192 771 Planarity : 0.004 0.028 789 Dihedral : 13.128 86.604 1644 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 0.00 % 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: 0.97 (0.35), residues: 582 helix: 1.64 (0.28), residues: 355 sheet: 0.82 (0.97), residues: 32 loop : -1.30 (0.42), residues: 195 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.522 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 1.4664 time to fit residues: 88.1884 Evaluate side-chains 46 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.485 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.0050 chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 overall best weight: 1.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN B 491 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 4632 Z= 0.217 Angle : 0.525 6.386 6295 Z= 0.266 Chirality : 0.040 0.124 771 Planarity : 0.004 0.029 789 Dihedral : 3.820 15.837 653 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 2.39 % 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: 0.67 (0.35), residues: 582 helix: 1.35 (0.28), residues: 354 sheet: 0.52 (0.94), residues: 32 loop : -1.24 (0.42), residues: 196 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 45 time to evaluate : 0.557 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 52 average time/residue: 1.4696 time to fit residues: 79.2848 Evaluate side-chains 47 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.556 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.0657 time to fit residues: 0.9574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 335 ASN B 491 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 4632 Z= 0.186 Angle : 0.472 5.710 6295 Z= 0.243 Chirality : 0.039 0.127 771 Planarity : 0.004 0.029 789 Dihedral : 3.623 12.595 653 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer Outliers : 2.39 % 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: 0.65 (0.35), residues: 582 helix: 1.31 (0.28), residues: 353 sheet: 0.49 (0.94), residues: 32 loop : -1.17 (0.43), residues: 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 44 time to evaluate : 0.574 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 49 average time/residue: 1.5518 time to fit residues: 78.7917 Evaluate side-chains 47 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.553 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.0689 time to fit residues: 0.9743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 335 ASN B 491 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 4632 Z= 0.261 Angle : 0.536 5.868 6295 Z= 0.275 Chirality : 0.041 0.129 771 Planarity : 0.004 0.032 789 Dihedral : 3.841 14.333 653 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 3.04 % 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: 0.38 (0.35), residues: 582 helix: 1.07 (0.28), residues: 353 sheet: 0.35 (0.95), residues: 32 loop : -1.24 (0.42), residues: 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 42 time to evaluate : 0.574 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 50 average time/residue: 1.5423 time to fit residues: 79.9271 Evaluate side-chains 45 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.559 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.0507 time to fit residues: 0.8155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 335 ASN B 491 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.032 4632 Z= 0.354 Angle : 0.610 6.723 6295 Z= 0.314 Chirality : 0.044 0.133 771 Planarity : 0.005 0.034 789 Dihedral : 4.118 16.156 653 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 2.39 % 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: 0.08 (0.34), residues: 582 helix: 0.80 (0.27), residues: 351 sheet: 0.20 (0.94), residues: 32 loop : -1.25 (0.43), residues: 199 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 43 time to evaluate : 0.574 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 50 average time/residue: 1.4349 time to fit residues: 74.2505 Evaluate side-chains 47 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 0.410 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.0481 time to fit residues: 0.7966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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: