Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 09:17:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rto_24685/04_2023/7rto_24685.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rto_24685/04_2023/7rto_24685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rto_24685/04_2023/7rto_24685.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rto_24685/04_2023/7rto_24685.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rto_24685/04_2023/7rto_24685.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rto_24685/04_2023/7rto_24685.pdb" } resolution = 3.8 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= 0.002 sd= 0.009 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: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 4160 2.51 5 N 1205 2.21 5 O 1228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 82": "OE1" <-> "OE2" Residue "A GLU 103": "OE1" <-> "OE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 400": "OD1" <-> "OD2" Residue "A ASP 406": "OD1" <-> "OD2" Residue "A GLU 427": "OE1" <-> "OE2" Residue "B TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 104": "OD1" <-> "OD2" Residue "B TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 6607 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2006 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 10, 'TRANS': 259} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "B" Number of atoms: 2595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2595 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 10, 'TRANS': 337} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 270 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 116 Chain: "C" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2006 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 10, 'TRANS': 259} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 92 Time building chain proxies: 4.13, per 1000 atoms: 0.63 Number of scatterers: 6607 At special positions: 0 Unit cell: (104.72, 110.16, 114.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 1228 8.00 N 1205 7.00 C 4160 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: 2.54 Conformation dependent library (CDL) restraints added in 1.2 seconds 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1664 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 6 sheets defined 61.3% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 64 through 80 removed outlier: 3.716A pdb=" N SER A 68 " --> pdb=" O SER A 64 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER A 80 " --> pdb=" O ASN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 135 removed outlier: 3.558A pdb=" N ARG A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 340 Proline residue: A 326 - end of helix Processing helix chain 'A' and resid 346 through 353 removed outlier: 3.820A pdb=" N VAL A 350 " --> pdb=" O ILE A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 438 Processing helix chain 'A' and resid 445 through 455 removed outlier: 3.575A pdb=" N ARG A 449 " --> pdb=" O MET A 445 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR A 455 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 483 Processing helix chain 'A' and resid 483 through 491 removed outlier: 3.724A pdb=" N GLN A 487 " --> pdb=" O ASP A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 509 Processing helix chain 'B' and resid 65 through 79 Processing helix chain 'B' and resid 89 through 115 removed outlier: 4.241A pdb=" N TYR B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 135 removed outlier: 7.576A pdb=" N LYS B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLU B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B 127 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL B 130 " --> pdb=" O GLU B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 177 Processing helix chain 'B' and resid 184 through 204 Processing helix chain 'B' and resid 249 through 256 removed outlier: 3.902A pdb=" N GLU B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 263 Processing helix chain 'B' and resid 296 through 330 Proline residue: B 326 - end of helix Processing helix chain 'B' and resid 424 through 438 Processing helix chain 'B' and resid 445 through 454 Processing helix chain 'B' and resid 469 through 482 Processing helix chain 'B' and resid 483 through 491 removed outlier: 3.572A pdb=" N GLN B 487 " --> pdb=" O ASP B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 509 Processing helix chain 'B' and resid 510 through 513 Processing helix chain 'C' and resid 65 through 79 Processing helix chain 'C' and resid 89 through 135 removed outlier: 4.531A pdb=" N ASN C 135 " --> pdb=" O TYR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 340 Proline residue: C 326 - end of helix removed outlier: 4.211A pdb=" N GLY C 340 " --> pdb=" O LYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 343 No H-bonds generated for 'chain 'C' and resid 341 through 343' Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'C' and resid 424 through 438 removed outlier: 3.524A pdb=" N SER C 438 " --> pdb=" O ASN C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 454 Processing helix chain 'C' and resid 469 through 483 Processing helix chain 'C' and resid 484 through 491 removed outlier: 3.786A pdb=" N HIS C 489 " --> pdb=" O GLU C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 509 Processing sheet with id=AA1, first strand: chain 'A' and resid 401 through 406 removed outlier: 3.721A pdb=" N GLY A 462 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N SER A 368 " --> pdb=" O TYR A 460 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N TYR A 460 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 410 through 414 Processing sheet with id=AA3, first strand: chain 'B' and resid 401 through 408 removed outlier: 3.884A pdb=" N GLY B 462 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER B 368 " --> pdb=" O TYR B 460 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N TYR B 460 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 412 through 414 Processing sheet with id=AA5, first strand: chain 'C' and resid 401 through 406 removed outlier: 4.085A pdb=" N GLY C 462 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N SER C 368 " --> pdb=" O TYR C 460 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N TYR C 460 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 410 through 414 468 hydrogen bonds defined for protein. 1362 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: 1.99 Time building geometry restraints manager: 2.76 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: 2122 1.34 - 1.45: 955 1.45 - 1.57: 3635 1.57 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 6734 Sorted by residual: bond pdb=" N GLN A 360 " pdb=" CA GLN A 360 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.33e-02 5.65e+03 6.65e+00 bond pdb=" N ASP A 406 " pdb=" CA ASP A 406 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.31e-02 5.83e+03 6.35e+00 bond pdb=" N LEU C 113 " pdb=" CA LEU C 113 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.52e+00 bond pdb=" CG1 ILE C 490 " pdb=" CD1 ILE C 490 " ideal model delta sigma weight residual 1.513 1.451 0.062 3.90e-02 6.57e+02 2.50e+00 bond pdb=" CB GLN C 361 " pdb=" CG GLN C 361 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.94e+00 ... (remaining 6729 not shown) Histogram of bond angle deviations from ideal: 100.05 - 106.84: 168 106.84 - 113.62: 3675 113.62 - 120.41: 2589 120.41 - 127.20: 2626 127.20 - 133.98: 72 Bond angle restraints: 9130 Sorted by residual: angle pdb=" O GLN A 360 " pdb=" C GLN A 360 " pdb=" N GLN A 361 " ideal model delta sigma weight residual 122.18 125.88 -3.70 9.90e-01 1.02e+00 1.39e+01 angle pdb=" CB LYS A 511 " pdb=" CG LYS A 511 " pdb=" CD LYS A 511 " ideal model delta sigma weight residual 111.30 119.34 -8.04 2.30e+00 1.89e-01 1.22e+01 angle pdb=" CG1 ILE C 356 " pdb=" CB ILE C 356 " pdb=" CG2 ILE C 356 " ideal model delta sigma weight residual 110.70 101.37 9.33 3.00e+00 1.11e-01 9.68e+00 angle pdb=" CA GLN C 478 " pdb=" CB GLN C 478 " pdb=" CG GLN C 478 " ideal model delta sigma weight residual 114.10 120.15 -6.05 2.00e+00 2.50e-01 9.16e+00 angle pdb=" C ALA C 359 " pdb=" N GLN C 360 " pdb=" CA GLN C 360 " ideal model delta sigma weight residual 122.23 126.83 -4.60 1.57e+00 4.06e-01 8.59e+00 ... (remaining 9125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 3603 17.85 - 35.69: 322 35.69 - 53.53: 58 53.53 - 71.38: 9 71.38 - 89.22: 6 Dihedral angle restraints: 3998 sinusoidal: 1429 harmonic: 2569 Sorted by residual: dihedral pdb=" CA TYR C 65 " pdb=" C TYR C 65 " pdb=" N GLY C 66 " pdb=" CA GLY C 66 " ideal model delta harmonic sigma weight residual -180.00 -157.44 -22.56 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA HIS A 385 " pdb=" C HIS A 385 " pdb=" N HIS A 386 " pdb=" CA HIS A 386 " ideal model delta harmonic sigma weight residual 180.00 157.58 22.42 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA TYR B 404 " pdb=" C TYR B 404 " pdb=" N GLU B 405 " pdb=" CA GLU B 405 " ideal model delta harmonic sigma weight residual 180.00 159.48 20.52 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 3995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 955 0.090 - 0.179: 61 0.179 - 0.269: 8 0.269 - 0.359: 0 0.359 - 0.448: 1 Chirality restraints: 1025 Sorted by residual: chirality pdb=" CB ILE A 356 " pdb=" CA ILE A 356 " pdb=" CG1 ILE A 356 " pdb=" CG2 ILE A 356 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 5.02e+00 chirality pdb=" CB ILE C 356 " pdb=" CA ILE C 356 " pdb=" CG1 ILE C 356 " pdb=" CG2 ILE C 356 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA ILE C 364 " pdb=" N ILE C 364 " pdb=" C ILE C 364 " pdb=" CB ILE C 364 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 1022 not shown) Planarity restraints: 1206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 448 " 0.023 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C ARG A 448 " -0.079 2.00e-02 2.50e+03 pdb=" O ARG A 448 " 0.029 2.00e-02 2.50e+03 pdb=" N ARG A 449 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 466 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.98e+00 pdb=" C TYR C 466 " 0.046 2.00e-02 2.50e+03 pdb=" O TYR C 466 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP C 467 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 477 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.58e+00 pdb=" C ALA C 477 " 0.041 2.00e-02 2.50e+03 pdb=" O ALA C 477 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN C 478 " -0.014 2.00e-02 2.50e+03 ... (remaining 1203 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 537 2.74 - 3.28: 6560 3.28 - 3.82: 10786 3.82 - 4.36: 11393 4.36 - 4.90: 20404 Nonbonded interactions: 49680 Sorted by model distance: nonbonded pdb=" O GLY A 493 " pdb=" NE2 GLN A 498 " model vdw 2.200 2.520 nonbonded pdb=" O LEU A 450 " pdb=" OG SER A 453 " model vdw 2.328 2.440 nonbonded pdb=" O HIS A 384 " pdb=" ND1 HIS A 385 " model vdw 2.336 2.520 nonbonded pdb=" O ALA A 369 " pdb=" OG SER A 373 " model vdw 2.356 2.440 nonbonded pdb=" O SER C 89 " pdb=" OG SER C 89 " model vdw 2.385 2.440 ... (remaining 49675 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 'C' } 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 group one per residue 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: 1.110 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: 6.260 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 21.250 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 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 : 0.004 0.062 6734 Z= 0.243 Angle : 0.821 9.484 9130 Z= 0.449 Chirality : 0.052 0.448 1025 Planarity : 0.005 0.045 1206 Dihedral : 14.320 89.223 2334 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer Outliers : 0.16 % 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: 1.09 (0.30), residues: 870 helix: 2.41 (0.23), residues: 490 sheet: -0.19 (0.49), residues: 124 loop : -2.30 (0.37), residues: 256 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 0.873 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.1973 time to fit residues: 36.0240 Evaluate side-chains 92 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.736 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 7.9990 chunk 66 optimal weight: 0.2980 chunk 37 optimal weight: 30.0000 chunk 22 optimal weight: 7.9990 chunk 44 optimal weight: 30.0000 chunk 35 optimal weight: 40.0000 chunk 68 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 41 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 79 optimal weight: 9.9990 overall best weight: 6.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 HIS B 108 ASN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 6734 Z= 0.251 Angle : 0.613 6.958 9130 Z= 0.331 Chirality : 0.043 0.188 1025 Planarity : 0.004 0.027 1206 Dihedral : 4.447 20.901 951 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer Outliers : 1.97 % 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: 1.38 (0.30), residues: 870 helix: 2.43 (0.23), residues: 505 sheet: 0.16 (0.48), residues: 128 loop : -2.15 (0.39), residues: 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 0.814 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 11 residues processed: 105 average time/residue: 0.1491 time to fit residues: 22.3439 Evaluate side-chains 102 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 0.807 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0640 time to fit residues: 2.3723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 54 optimal weight: 30.0000 chunk 22 optimal weight: 9.9990 chunk 80 optimal weight: 20.0000 chunk 86 optimal weight: 5.9990 chunk 71 optimal weight: 30.0000 chunk 79 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 HIS ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 6734 Z= 0.306 Angle : 0.628 7.252 9130 Z= 0.339 Chirality : 0.044 0.206 1025 Planarity : 0.004 0.028 1206 Dihedral : 4.695 20.613 951 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer Outliers : 1.15 % 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: 1.11 (0.29), residues: 870 helix: 2.33 (0.23), residues: 497 sheet: -0.10 (0.47), residues: 128 loop : -2.32 (0.37), residues: 245 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 0.800 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 101 average time/residue: 0.1558 time to fit residues: 22.2131 Evaluate side-chains 92 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.790 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0666 time to fit residues: 1.8054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 38 optimal weight: 40.0000 chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 76 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 HIS ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 6734 Z= 0.233 Angle : 0.575 6.978 9130 Z= 0.312 Chirality : 0.042 0.197 1025 Planarity : 0.003 0.025 1206 Dihedral : 4.440 19.093 951 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer Outliers : 1.15 % 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: 1.18 (0.29), residues: 870 helix: 2.30 (0.23), residues: 509 sheet: -0.08 (0.47), residues: 128 loop : -2.31 (0.38), residues: 233 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 0.849 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 101 average time/residue: 0.1606 time to fit residues: 22.8490 Evaluate side-chains 92 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 0.816 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0615 time to fit residues: 1.8961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 5.9990 chunk 1 optimal weight: 0.0970 chunk 63 optimal weight: 8.9990 chunk 35 optimal weight: 30.0000 chunk 72 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 overall best weight: 4.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 HIS ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 6734 Z= 0.207 Angle : 0.565 7.040 9130 Z= 0.303 Chirality : 0.041 0.194 1025 Planarity : 0.003 0.024 1206 Dihedral : 4.314 18.477 951 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer Outliers : 1.15 % 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: 1.27 (0.30), residues: 870 helix: 2.40 (0.23), residues: 511 sheet: -0.19 (0.46), residues: 128 loop : -2.27 (0.38), residues: 231 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 0.739 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 107 average time/residue: 0.1486 time to fit residues: 22.5358 Evaluate side-chains 95 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 91 time to evaluate : 0.749 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0775 time to fit residues: 1.5479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 85 optimal weight: 8.9990 chunk 70 optimal weight: 40.0000 chunk 39 optimal weight: 20.0000 chunk 7 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 chunk 44 optimal weight: 20.0000 chunk 82 optimal weight: 9.9990 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 HIS ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 6734 Z= 0.243 Angle : 0.596 7.898 9130 Z= 0.318 Chirality : 0.043 0.310 1025 Planarity : 0.003 0.025 1206 Dihedral : 4.381 18.925 951 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer Outliers : 1.80 % 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: 1.16 (0.29), residues: 870 helix: 2.31 (0.22), residues: 511 sheet: -0.25 (0.46), residues: 128 loop : -2.29 (0.38), residues: 231 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 10 residues processed: 99 average time/residue: 0.1573 time to fit residues: 22.1888 Evaluate side-chains 98 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 0.783 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0718 time to fit residues: 2.3749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.0970 chunk 48 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 51 optimal weight: 20.0000 chunk 39 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 overall best weight: 3.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 HIS ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 6734 Z= 0.177 Angle : 0.562 7.243 9130 Z= 0.298 Chirality : 0.041 0.283 1025 Planarity : 0.003 0.026 1206 Dihedral : 4.188 17.080 951 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer Outliers : 0.33 % 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: 1.42 (0.30), residues: 870 helix: 2.54 (0.23), residues: 511 sheet: -0.16 (0.47), residues: 128 loop : -2.23 (0.38), residues: 231 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 0.848 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 100 average time/residue: 0.1578 time to fit residues: 22.4769 Evaluate side-chains 92 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.739 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 7 optimal weight: 0.0980 chunk 66 optimal weight: 6.9990 chunk 77 optimal weight: 30.0000 chunk 81 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 overall best weight: 4.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 HIS ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 6734 Z= 0.202 Angle : 0.574 7.310 9130 Z= 0.305 Chirality : 0.043 0.475 1025 Planarity : 0.003 0.022 1206 Dihedral : 4.207 17.526 951 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer Outliers : 0.33 % 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: 1.44 (0.29), residues: 870 helix: 2.53 (0.22), residues: 511 sheet: 0.01 (0.48), residues: 125 loop : -2.25 (0.38), residues: 234 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 0.816 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 94 average time/residue: 0.1496 time to fit residues: 20.2702 Evaluate side-chains 92 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 90 time to evaluate : 0.812 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0790 time to fit residues: 1.3362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 34 optimal weight: 0.1980 chunk 62 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 chunk 74 optimal weight: 20.0000 chunk 78 optimal weight: 6.9990 chunk 51 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 HIS ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 6734 Z= 0.210 Angle : 0.588 9.082 9130 Z= 0.312 Chirality : 0.042 0.321 1025 Planarity : 0.003 0.023 1206 Dihedral : 4.231 17.495 951 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer Outliers : 0.82 % 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: 1.36 (0.29), residues: 870 helix: 2.46 (0.22), residues: 512 sheet: -0.02 (0.47), residues: 125 loop : -2.31 (0.38), residues: 233 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 0.856 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 92 average time/residue: 0.1575 time to fit residues: 20.7205 Evaluate side-chains 91 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 88 time to evaluate : 0.812 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0631 time to fit residues: 1.4572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 87 optimal weight: 0.5980 chunk 80 optimal weight: 20.0000 chunk 69 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 overall best weight: 6.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 HIS ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 6734 Z= 0.277 Angle : 0.653 11.710 9130 Z= 0.342 Chirality : 0.044 0.326 1025 Planarity : 0.003 0.025 1206 Dihedral : 4.456 19.167 951 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer Outliers : 0.33 % 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: 1.15 (0.29), residues: 870 helix: 2.31 (0.22), residues: 509 sheet: -0.23 (0.48), residues: 126 loop : -2.29 (0.38), residues: 235 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 0.821 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 84 average time/residue: 0.1561 time to fit residues: 18.9724 Evaluate side-chains 81 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 0.830 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0646 time to fit residues: 1.2542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 0.0030 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 69 optimal weight: 30.0000 chunk 29 optimal weight: 0.7980 chunk 71 optimal weight: 0.0070 chunk 8 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 3 optimal weight: 20.0000 overall best weight: 0.5008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 HIS ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.159147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.135747 restraints weight = 11900.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.133887 restraints weight = 10935.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.134398 restraints weight = 10212.610| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 6734 Z= 0.145 Angle : 0.576 10.186 9130 Z= 0.301 Chirality : 0.041 0.324 1025 Planarity : 0.003 0.020 1206 Dihedral : 3.959 16.835 951 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer Outliers : 0.16 % 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: 1.55 (0.30), residues: 870 helix: 2.67 (0.22), residues: 507 sheet: -0.14 (0.47), residues: 133 loop : -2.18 (0.39), residues: 230 =============================================================================== Job complete usr+sys time: 1187.55 seconds wall clock time: 22 minutes 29.00 seconds (1349.00 seconds total)