Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 2 21:00:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dha_27434/10_2023/8dha_27434.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dha_27434/10_2023/8dha_27434.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/8dha_27434/10_2023/8dha_27434.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dha_27434/10_2023/8dha_27434.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dha_27434/10_2023/8dha_27434.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dha_27434/10_2023/8dha_27434.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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 16 5.16 5 C 2234 2.51 5 N 596 2.21 5 O 664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 435": "OE1" <-> "OE2" Residue "B TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 495": "OE1" <-> "OE2" Residue "B PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 85": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 3510 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 773 Classifications: {'peptide': 94} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 89} Chain: "B" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1622 Classifications: {'peptide': 204} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 188} Chain: "C" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1087 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.54, per 1000 atoms: 0.72 Number of scatterers: 3510 At special positions: 0 Unit cell: (103.786, 72.7693, 95.4352, 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 16 16.00 O 664 8.00 N 596 7.00 C 2234 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 410 " distance=2.03 Simple disulfide: pdb=" SG CYS A 411 " - pdb=" SG CYS A 416 " distance=2.03 Simple disulfide: pdb=" SG CYS B 434 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 526 " distance=2.03 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 496 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 345 " " NAG B 901 " - " ASN B 622 " Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 509.1 milliseconds 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 844 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 9 sheets defined 25.7% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'B' and resid 528 through 533 removed outlier: 3.739A pdb=" N VAL B 532 " --> pdb=" O PRO B 529 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL B 533 " --> pdb=" O ASP B 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 26 Processing helix chain 'C' and resid 50 through 67 Processing helix chain 'C' and resid 70 through 94 Processing helix chain 'C' and resid 107 through 117 removed outlier: 3.554A pdb=" N ASP C 111 " --> pdb=" O PRO C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 141 removed outlier: 4.393A pdb=" N ASP C 141 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 337 through 339 removed outlier: 5.963A pdb=" N ILE A 338 " --> pdb=" O TYR A 424 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 408 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 365 " --> pdb=" O CYS A 411 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 337 through 339 removed outlier: 5.963A pdb=" N ILE A 338 " --> pdb=" O TYR A 424 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 408 " --> pdb=" O ALA A 421 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 346 through 347 removed outlier: 3.788A pdb=" N ALA A 346 " --> pdb=" O PHE A 391 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AA5, first strand: chain 'B' and resid 432 through 436 removed outlier: 3.516A pdb=" N MET B 443 " --> pdb=" O PHE B 498 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS B 445 " --> pdb=" O CYS B 496 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N CYS B 496 " --> pdb=" O CYS B 445 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TRP B 447 " --> pdb=" O TYR B 494 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR B 494 " --> pdb=" O TRP B 447 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 482 through 483 removed outlier: 3.768A pdb=" N THR B 459 " --> pdb=" O ASN B 514 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN B 514 " --> pdb=" O THR B 459 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN B 461 " --> pdb=" O ARG B 512 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG B 512 " --> pdb=" O GLN B 461 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG B 463 " --> pdb=" O TRP B 510 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B 520 " --> pdb=" O ILE B 513 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N HIS B 515 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY B 518 " --> pdb=" O HIS B 515 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 482 through 483 removed outlier: 3.768A pdb=" N THR B 459 " --> pdb=" O ASN B 514 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN B 514 " --> pdb=" O THR B 459 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN B 461 " --> pdb=" O ARG B 512 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG B 512 " --> pdb=" O GLN B 461 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG B 463 " --> pdb=" O TRP B 510 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR B 507 " --> pdb=" O VAL B 527 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL B 527 " --> pdb=" O TYR B 507 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N MET B 509 " --> pdb=" O THR B 525 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR B 525 " --> pdb=" O MET B 509 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 542 through 545 removed outlier: 3.816A pdb=" N LYS B 542 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER B 555 " --> pdb=" O LYS B 542 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL B 554 " --> pdb=" O ALA B 594 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 582 through 586 removed outlier: 3.933A pdb=" N VAL B 607 " --> pdb=" O ALA B 627 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA B 627 " --> pdb=" O VAL B 607 " (cutoff:3.500A) 137 hydrogen bonds defined for protein. 375 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.92 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1122 1.34 - 1.46: 788 1.46 - 1.58: 1658 1.58 - 1.70: 1 1.70 - 1.81: 19 Bond restraints: 3588 Sorted by residual: bond pdb=" CB PRO B 472 " pdb=" CG PRO B 472 " ideal model delta sigma weight residual 1.492 1.614 -0.122 5.00e-02 4.00e+02 5.94e+00 bond pdb=" C2 NAG A 901 " pdb=" N2 NAG A 901 " ideal model delta sigma weight residual 1.439 1.463 -0.024 2.00e-02 2.50e+03 1.40e+00 bond pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.39e+00 bond pdb=" C5 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.14e+00 bond pdb=" C5 NAG B 901 " pdb=" O5 NAG B 901 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.10e+00 ... (remaining 3583 not shown) Histogram of bond angle deviations from ideal: 98.82 - 105.87: 80 105.87 - 112.93: 2021 112.93 - 119.98: 1144 119.98 - 127.04: 1586 127.04 - 134.10: 53 Bond angle restraints: 4884 Sorted by residual: angle pdb=" CA SER B 450 " pdb=" C SER B 450 " pdb=" N THR B 451 " ideal model delta sigma weight residual 116.84 125.69 -8.85 1.71e+00 3.42e-01 2.68e+01 angle pdb=" CA PRO B 472 " pdb=" N PRO B 472 " pdb=" CD PRO B 472 " ideal model delta sigma weight residual 112.00 104.86 7.14 1.40e+00 5.10e-01 2.60e+01 angle pdb=" CA SER B 450 " pdb=" C SER B 450 " pdb=" O SER B 450 " ideal model delta sigma weight residual 120.51 115.41 5.10 1.43e+00 4.89e-01 1.27e+01 angle pdb=" N LYS C 5 " pdb=" CA LYS C 5 " pdb=" C LYS C 5 " ideal model delta sigma weight residual 111.28 107.66 3.62 1.09e+00 8.42e-01 1.10e+01 angle pdb=" CA LEU C 104 " pdb=" CB LEU C 104 " pdb=" CG LEU C 104 " ideal model delta sigma weight residual 116.30 127.41 -11.11 3.50e+00 8.16e-02 1.01e+01 ... (remaining 4879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 1833 17.93 - 35.86: 279 35.86 - 53.79: 52 53.79 - 71.72: 7 71.72 - 89.64: 4 Dihedral angle restraints: 2175 sinusoidal: 877 harmonic: 1298 Sorted by residual: dihedral pdb=" CB CYS B 486 " pdb=" SG CYS B 486 " pdb=" SG CYS B 496 " pdb=" CB CYS B 496 " ideal model delta sinusoidal sigma weight residual 93.00 55.09 37.91 1 1.00e+01 1.00e-02 2.03e+01 dihedral pdb=" CB GLU B 435 " pdb=" CG GLU B 435 " pdb=" CD GLU B 435 " pdb=" OE1 GLU B 435 " ideal model delta sinusoidal sigma weight residual 0.00 89.64 -89.64 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG C 35 " pdb=" CD ARG C 35 " pdb=" NE ARG C 35 " pdb=" CZ ARG C 35 " ideal model delta sinusoidal sigma weight residual -180.00 -135.34 -44.66 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 2172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 381 0.039 - 0.077: 135 0.077 - 0.116: 47 0.116 - 0.154: 7 0.154 - 0.193: 2 Chirality restraints: 572 Sorted by residual: chirality pdb=" C1 NAG B 901 " pdb=" ND2 ASN B 622 " pdb=" C2 NAG B 901 " pdb=" O5 NAG B 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.29e-01 chirality pdb=" C2 NAG A 901 " pdb=" C1 NAG A 901 " pdb=" C3 NAG A 901 " pdb=" N2 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.49 -2.31 -0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CB VAL C 113 " pdb=" CA VAL C 113 " pdb=" CG1 VAL C 113 " pdb=" CG2 VAL C 113 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.01e-01 ... (remaining 569 not shown) Planarity restraints: 616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 471 " 0.048 5.00e-02 4.00e+02 6.92e-02 7.67e+00 pdb=" N PRO B 472 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 472 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 472 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 374 " 0.038 5.00e-02 4.00e+02 5.81e-02 5.39e+00 pdb=" N PRO A 375 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 447 " 0.012 2.00e-02 2.50e+03 1.21e-02 3.66e+00 pdb=" CG TRP B 447 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP B 447 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP B 447 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 447 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 447 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 447 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 447 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 447 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 447 " 0.002 2.00e-02 2.50e+03 ... (remaining 613 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 139 2.70 - 3.25: 3307 3.25 - 3.80: 5152 3.80 - 4.35: 5698 4.35 - 4.90: 9630 Nonbonded interactions: 23926 Sorted by model distance: nonbonded pdb=" OE2 GLU B 563 " pdb=" OG1 THR C 19 " model vdw 2.155 2.440 nonbonded pdb=" O VAL C 64 " pdb=" OG SER C 67 " model vdw 2.216 2.440 nonbonded pdb=" O LEU B 455 " pdb=" OG SER B 458 " model vdw 2.223 2.440 nonbonded pdb=" OH TYR B 470 " pdb=" OD2 ASP C 9 " model vdw 2.238 2.440 nonbonded pdb=" O ILE B 511 " pdb=" OG SER B 522 " model vdw 2.304 2.440 ... (remaining 23921 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=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: 1.500 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: 6.510 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 14.270 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 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 0.122 3588 Z= 0.230 Angle : 0.763 11.108 4884 Z= 0.392 Chirality : 0.045 0.193 572 Planarity : 0.005 0.069 614 Dihedral : 16.996 89.644 1316 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.49 % Allowed : 34.07 % Favored : 65.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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 (0.41), residues: 433 helix: 2.17 (0.52), residues: 106 sheet: 0.30 (0.54), residues: 103 loop : -1.15 (0.41), residues: 224 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 87 average time/residue: 0.1553 time to fit residues: 16.5403 Evaluate side-chains 80 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 0.431 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0612 time to fit residues: 0.6654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN B 608 GLN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 3588 Z= 0.434 Angle : 0.814 8.418 4884 Z= 0.415 Chirality : 0.049 0.221 572 Planarity : 0.006 0.050 614 Dihedral : 5.079 17.058 473 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 7.16 % Allowed : 28.40 % Favored : 64.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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: -0.51 (0.40), residues: 433 helix: 1.72 (0.49), residues: 110 sheet: 0.11 (0.54), residues: 95 loop : -1.66 (0.39), residues: 228 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 76 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 16 residues processed: 98 average time/residue: 0.1446 time to fit residues: 17.6741 Evaluate side-chains 85 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 69 time to evaluate : 0.435 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0378 time to fit residues: 1.6378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 26 optimal weight: 0.0070 chunk 10 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 31 optimal weight: 4.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 ASN C 28 GLN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3588 Z= 0.222 Angle : 0.714 9.150 4884 Z= 0.349 Chirality : 0.047 0.237 572 Planarity : 0.004 0.046 614 Dihedral : 4.696 15.958 473 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.69 % Allowed : 29.88 % Favored : 65.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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: -0.42 (0.41), residues: 433 helix: 2.02 (0.51), residues: 110 sheet: -0.08 (0.51), residues: 102 loop : -1.65 (0.40), residues: 221 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 5 residues processed: 92 average time/residue: 0.1527 time to fit residues: 17.4395 Evaluate side-chains 75 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.391 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0517 time to fit residues: 0.9609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3588 Z= 0.315 Angle : 0.739 8.867 4884 Z= 0.369 Chirality : 0.047 0.234 572 Planarity : 0.005 0.045 614 Dihedral : 4.898 17.443 473 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 3.21 % Allowed : 31.85 % Favored : 64.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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: -0.62 (0.41), residues: 433 helix: 1.92 (0.51), residues: 110 sheet: -0.34 (0.52), residues: 100 loop : -1.72 (0.40), residues: 223 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.426 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 83 average time/residue: 0.1478 time to fit residues: 15.4011 Evaluate side-chains 81 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 71 time to evaluate : 0.436 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0364 time to fit residues: 1.2250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3588 Z= 0.309 Angle : 0.740 9.148 4884 Z= 0.368 Chirality : 0.046 0.238 572 Planarity : 0.005 0.044 614 Dihedral : 4.909 18.357 473 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 3.21 % Allowed : 33.33 % Favored : 63.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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: -0.71 (0.41), residues: 433 helix: 1.88 (0.51), residues: 110 sheet: -0.46 (0.53), residues: 100 loop : -1.76 (0.40), residues: 223 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 84 average time/residue: 0.1319 time to fit residues: 14.0699 Evaluate side-chains 77 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 70 time to evaluate : 0.321 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0330 time to fit residues: 0.8164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.8980 chunk 10 optimal weight: 0.0370 chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 3 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3588 Z= 0.204 Angle : 0.717 12.153 4884 Z= 0.340 Chirality : 0.045 0.243 572 Planarity : 0.004 0.042 614 Dihedral : 4.629 18.240 473 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 1.23 % Allowed : 34.81 % Favored : 63.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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: -0.41 (0.41), residues: 433 helix: 2.05 (0.51), residues: 110 sheet: -0.17 (0.53), residues: 97 loop : -1.57 (0.40), residues: 226 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 80 average time/residue: 0.1363 time to fit residues: 13.7495 Evaluate side-chains 73 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 0.452 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0366 time to fit residues: 0.7398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3588 Z= 0.224 Angle : 0.707 9.953 4884 Z= 0.338 Chirality : 0.047 0.263 572 Planarity : 0.004 0.043 614 Dihedral : 4.636 19.368 473 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 1.73 % Allowed : 36.05 % Favored : 62.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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: -0.41 (0.41), residues: 433 helix: 2.01 (0.52), residues: 110 sheet: -0.34 (0.53), residues: 100 loop : -1.47 (0.40), residues: 223 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 82 average time/residue: 0.1407 time to fit residues: 14.6303 Evaluate side-chains 76 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 0.444 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0350 time to fit residues: 0.7768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3588 Z= 0.229 Angle : 0.748 10.547 4884 Z= 0.354 Chirality : 0.046 0.242 572 Planarity : 0.004 0.044 614 Dihedral : 4.682 19.105 473 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.48 % Allowed : 35.80 % Favored : 62.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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: -0.40 (0.41), residues: 433 helix: 2.02 (0.52), residues: 110 sheet: -0.36 (0.53), residues: 100 loop : -1.44 (0.40), residues: 223 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 76 average time/residue: 0.1405 time to fit residues: 13.5251 Evaluate side-chains 73 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 0.435 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0358 time to fit residues: 0.7676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 24 optimal weight: 0.2980 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 0.0170 chunk 42 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3588 Z= 0.189 Angle : 0.725 9.831 4884 Z= 0.339 Chirality : 0.046 0.245 572 Planarity : 0.004 0.043 614 Dihedral : 4.544 18.989 473 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.74 % Allowed : 36.30 % Favored : 62.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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: -0.42 (0.41), residues: 433 helix: 2.00 (0.52), residues: 110 sheet: -0.46 (0.52), residues: 98 loop : -1.40 (0.40), residues: 225 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 74 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 76 average time/residue: 0.1401 time to fit residues: 13.4188 Evaluate side-chains 75 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 0.396 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0345 time to fit residues: 0.7524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 26 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3588 Z= 0.223 Angle : 0.738 10.646 4884 Z= 0.348 Chirality : 0.046 0.238 572 Planarity : 0.004 0.043 614 Dihedral : 4.671 19.693 473 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.25 % Allowed : 35.80 % Favored : 63.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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: -0.46 (0.41), residues: 433 helix: 1.92 (0.51), residues: 110 sheet: -0.46 (0.52), residues: 98 loop : -1.41 (0.40), residues: 225 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 72 average time/residue: 0.1467 time to fit residues: 13.2809 Evaluate side-chains 70 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.434 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0669 time to fit residues: 0.7153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 499 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.107369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.073946 restraints weight = 10721.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.075682 restraints weight = 5842.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.076627 restraints weight = 4410.369| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3588 Z= 0.245 Angle : 0.741 10.439 4884 Z= 0.354 Chirality : 0.046 0.240 572 Planarity : 0.004 0.043 614 Dihedral : 4.699 19.225 473 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.49 % Allowed : 36.79 % Favored : 62.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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: -0.54 (0.41), residues: 433 helix: 1.87 (0.51), residues: 110 sheet: -0.54 (0.52), residues: 98 loop : -1.46 (0.40), residues: 225 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1227.85 seconds wall clock time: 22 minutes 48.42 seconds (1368.42 seconds total)