Starting phenix.real_space_refine on Sun Mar 10 16:25:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9i_22749/03_2024/7k9i_22749.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9i_22749/03_2024/7k9i_22749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9i_22749/03_2024/7k9i_22749.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9i_22749/03_2024/7k9i_22749.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9i_22749/03_2024/7k9i_22749.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9i_22749/03_2024/7k9i_22749.pdb" } resolution = 3.3 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= 0.002 sd= 0.053 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 2095 2.51 5 N 554 2.21 5 O 632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A ASP 442": "OD1" <-> "OD2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 89": "OD1" <-> "OD2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 7": "OE1" <-> "OE2" Residue "L GLU 40": "OE1" <-> "OE2" Residue "L PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 63": "NH1" <-> "NH2" Residue "L GLU 83": "OE1" <-> "OE2" Residue "L TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3295 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "H" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 926 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 812 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.30, per 1000 atoms: 0.70 Number of scatterers: 3295 At special positions: 0 Unit cell: (64.9, 85.8, 86.9, 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 632 8.00 N 554 7.00 C 2095 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " 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 601 " - " ASN A 343 " Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 679.9 milliseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 766 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 9 sheets defined 9.9% alpha, 36.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.605A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.200A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.896A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.277A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.569A pdb=" N THR H 90 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.703A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.834A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.306A pdb=" N THR H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.769A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR H 109 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.769A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.846A pdb=" N VAL L 18 " --> pdb=" O ILE L 77 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE L 77 " --> pdb=" O VAL L 18 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA L 74 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER L 67 " --> pdb=" O ALA L 74 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER L 65 " --> pdb=" O THR L 76 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 55 through 56 removed outlier: 3.754A pdb=" N LEU L 45 " --> pdb=" O LYS L 41 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY L 51 " --> pdb=" O ALA L 35 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ALA L 35 " --> pdb=" O GLY L 51 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 55 through 56 removed outlier: 3.754A pdb=" N LEU L 45 " --> pdb=" O LYS L 41 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY L 51 " --> pdb=" O ALA L 35 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ALA L 35 " --> pdb=" O GLY L 51 " (cutoff:3.500A) 119 hydrogen bonds defined for protein. 291 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: 0.85 Time building geometry restraints manager: 1.22 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: 1051 1.34 - 1.47: 910 1.47 - 1.59: 1402 1.59 - 1.71: 0 1.71 - 1.83: 16 Bond restraints: 3379 Sorted by residual: bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" C TYR A 505 " pdb=" N GLN A 506 " ideal model delta sigma weight residual 1.340 1.269 0.071 5.87e-02 2.90e+02 1.47e+00 bond pdb=" CB ASN L 36 " pdb=" CG ASN L 36 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.36e+00 bond pdb=" CB ILE A 434 " pdb=" CG2 ILE A 434 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.11e+00 bond pdb=" C3 NAG A 601 " pdb=" O3 NAG A 601 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 9.69e-01 ... (remaining 3374 not shown) Histogram of bond angle deviations from ideal: 100.51 - 107.21: 104 107.21 - 113.90: 1812 113.90 - 120.60: 1314 120.60 - 127.30: 1334 127.30 - 134.00: 37 Bond angle restraints: 4601 Sorted by residual: angle pdb=" CA CYS H 95 " pdb=" CB CYS H 95 " pdb=" SG CYS H 95 " ideal model delta sigma weight residual 114.40 120.30 -5.90 2.30e+00 1.89e-01 6.58e+00 angle pdb=" N CYS H 95 " pdb=" CA CYS H 95 " pdb=" C CYS H 95 " ideal model delta sigma weight residual 110.32 106.37 3.95 1.59e+00 3.96e-01 6.17e+00 angle pdb=" CA GLU A 516 " pdb=" CB GLU A 516 " pdb=" CG GLU A 516 " ideal model delta sigma weight residual 114.10 118.67 -4.57 2.00e+00 2.50e-01 5.23e+00 angle pdb=" C GLY L 52 " pdb=" N THR L 53 " pdb=" CA THR L 53 " ideal model delta sigma weight residual 121.54 125.86 -4.32 1.91e+00 2.74e-01 5.12e+00 angle pdb=" N GLY L 70 " pdb=" CA GLY L 70 " pdb=" C GLY L 70 " ideal model delta sigma weight residual 112.10 108.16 3.94 1.82e+00 3.02e-01 4.68e+00 ... (remaining 4596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 1821 17.83 - 35.66: 139 35.66 - 53.48: 17 53.48 - 71.31: 4 71.31 - 89.14: 2 Dihedral angle restraints: 1983 sinusoidal: 770 harmonic: 1213 Sorted by residual: dihedral pdb=" CB CYS L 22 " pdb=" SG CYS L 22 " pdb=" SG CYS L 90 " pdb=" CB CYS L 90 " ideal model delta sinusoidal sigma weight residual 93.00 51.32 41.68 1 1.00e+01 1.00e-02 2.43e+01 dihedral pdb=" CA TRP L 93 " pdb=" C TRP L 93 " pdb=" N TYR L 94 " pdb=" CA TYR L 94 " ideal model delta harmonic sigma weight residual 180.00 157.34 22.66 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 129.94 -36.94 1 1.00e+01 1.00e-02 1.93e+01 ... (remaining 1980 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 317 0.039 - 0.078: 118 0.078 - 0.116: 59 0.116 - 0.155: 8 0.155 - 0.193: 1 Chirality restraints: 503 Sorted by residual: chirality pdb=" CB THR A 430 " pdb=" CA THR A 430 " pdb=" OG1 THR A 430 " pdb=" CG2 THR A 430 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.35e-01 chirality pdb=" CB THR H 90 " pdb=" CA THR H 90 " pdb=" OG1 THR H 90 " pdb=" CG2 THR H 90 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" CA ILE L 87 " pdb=" N ILE L 87 " pdb=" C ILE L 87 " pdb=" CB ILE L 87 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.59e-01 ... (remaining 500 not shown) Planarity restraints: 592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 355 " -0.073 9.50e-02 1.11e+02 4.13e-02 8.64e+00 pdb=" NE ARG A 355 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 355 " -0.048 2.00e-02 2.50e+03 pdb=" NH1 ARG A 355 " 0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG A 355 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS L 41 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO L 42 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO L 42 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO L 42 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 462 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.78e+00 pdb=" N PRO A 463 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " -0.019 5.00e-02 4.00e+02 ... (remaining 589 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 72 2.67 - 3.23: 3219 3.23 - 3.79: 4886 3.79 - 4.34: 6660 4.34 - 4.90: 11314 Nonbonded interactions: 26151 Sorted by model distance: nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.118 2.440 nonbonded pdb=" O ILE H 30 " pdb=" OG1 THR H 53 " model vdw 2.140 2.440 nonbonded pdb=" NH1 ARG A 457 " pdb=" OD2 ASP A 467 " model vdw 2.173 2.520 nonbonded pdb=" OG1 THR L 12 " pdb=" O GLU L 16 " model vdw 2.189 2.440 nonbonded pdb=" OG SER H 17 " pdb=" O MET H 82 " model vdw 2.239 2.440 ... (remaining 26146 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.580 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 13.680 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 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 : 0.005 0.071 3379 Z= 0.361 Angle : 0.719 7.536 4601 Z= 0.385 Chirality : 0.049 0.193 503 Planarity : 0.005 0.043 591 Dihedral : 12.862 89.140 1199 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % 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: -0.86 (0.40), residues: 417 helix: -1.66 (0.85), residues: 32 sheet: 0.51 (0.45), residues: 133 loop : -1.05 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 47 HIS 0.003 0.001 HIS A 519 PHE 0.012 0.002 PHE A 490 TYR 0.015 0.001 TYR A 380 ARG 0.049 0.003 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 16 GLN cc_start: 0.7615 (pt0) cc_final: 0.7371 (pt0) REVERT: H 108 ASP cc_start: 0.7834 (t0) cc_final: 0.7624 (t0) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.2223 time to fit residues: 16.5282 Evaluate side-chains 54 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN H 3 GLN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3379 Z= 0.264 Angle : 0.679 7.009 4601 Z= 0.354 Chirality : 0.047 0.135 503 Planarity : 0.005 0.043 591 Dihedral : 6.801 54.726 485 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.13 % Allowed : 12.96 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.40), residues: 417 helix: -1.32 (0.95), residues: 33 sheet: 0.10 (0.44), residues: 142 loop : -0.85 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 47 HIS 0.001 0.001 HIS A 519 PHE 0.009 0.001 PHE A 490 TYR 0.011 0.001 TYR A 380 ARG 0.005 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8753 (mmtt) cc_final: 0.8500 (tppt) REVERT: A 420 ASP cc_start: 0.8213 (m-30) cc_final: 0.7661 (m-30) REVERT: L 7 GLU cc_start: 0.6558 (pm20) cc_final: 0.6305 (pm20) outliers start: 4 outliers final: 3 residues processed: 72 average time/residue: 0.1903 time to fit residues: 16.4683 Evaluate side-chains 66 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 117 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.3980 chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3379 Z= 0.181 Angle : 0.633 6.523 4601 Z= 0.322 Chirality : 0.045 0.136 503 Planarity : 0.004 0.037 591 Dihedral : 6.298 54.252 485 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.10 % Allowed : 16.34 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.40), residues: 417 helix: -1.42 (1.03), residues: 27 sheet: 0.25 (0.43), residues: 142 loop : -0.90 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 HIS 0.001 0.000 HIS A 519 PHE 0.006 0.001 PHE A 490 TYR 0.009 0.001 TYR A 380 ARG 0.005 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8726 (mmtt) cc_final: 0.8477 (tppt) REVERT: A 420 ASP cc_start: 0.8209 (m-30) cc_final: 0.7698 (m-30) REVERT: L 39 GLN cc_start: 0.7932 (tm-30) cc_final: 0.7542 (tm-30) outliers start: 11 outliers final: 5 residues processed: 76 average time/residue: 0.1897 time to fit residues: 17.1563 Evaluate side-chains 70 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 117 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 0.0980 chunk 10 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3379 Z= 0.259 Angle : 0.633 6.242 4601 Z= 0.326 Chirality : 0.045 0.135 503 Planarity : 0.004 0.039 591 Dihedral : 6.380 54.317 485 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.10 % Allowed : 18.59 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.40), residues: 417 helix: -1.50 (1.01), residues: 27 sheet: 0.37 (0.46), residues: 131 loop : -0.97 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 47 HIS 0.001 0.000 HIS A 519 PHE 0.009 0.001 PHE A 490 TYR 0.013 0.001 TYR A 380 ARG 0.006 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8748 (mmtt) cc_final: 0.8488 (tppt) REVERT: A 420 ASP cc_start: 0.8234 (m-30) cc_final: 0.7739 (m-30) outliers start: 11 outliers final: 10 residues processed: 75 average time/residue: 0.1687 time to fit residues: 15.1635 Evaluate side-chains 75 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 47 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 3379 Z= 0.327 Angle : 0.664 6.729 4601 Z= 0.343 Chirality : 0.046 0.146 503 Planarity : 0.005 0.043 591 Dihedral : 6.621 54.215 485 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 5.07 % Allowed : 18.31 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.40), residues: 417 helix: -1.58 (1.02), residues: 27 sheet: 0.30 (0.46), residues: 131 loop : -1.06 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.001 0.001 HIS L 97 PHE 0.011 0.001 PHE A 490 TYR 0.014 0.001 TYR A 380 ARG 0.006 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 68 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8729 (mmtt) cc_final: 0.8451 (tppt) REVERT: A 420 ASP cc_start: 0.8275 (m-30) cc_final: 0.7797 (m-30) outliers start: 18 outliers final: 14 residues processed: 80 average time/residue: 0.1711 time to fit residues: 16.5816 Evaluate side-chains 77 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 63 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 71 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 37 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3379 Z= 0.239 Angle : 0.648 7.017 4601 Z= 0.329 Chirality : 0.046 0.146 503 Planarity : 0.004 0.040 591 Dihedral : 6.402 54.477 485 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 5.63 % Allowed : 20.00 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.41), residues: 417 helix: -1.56 (1.00), residues: 27 sheet: -0.04 (0.44), residues: 141 loop : -0.88 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.001 0.001 HIS A 519 PHE 0.009 0.001 PHE A 490 TYR 0.011 0.001 TYR A 380 ARG 0.007 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 68 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8738 (mmtt) cc_final: 0.8456 (tppt) REVERT: A 420 ASP cc_start: 0.8250 (m-30) cc_final: 0.7769 (m-30) REVERT: A 517 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8194 (tt) outliers start: 20 outliers final: 15 residues processed: 81 average time/residue: 0.1683 time to fit residues: 16.4704 Evaluate side-chains 80 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 64 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 71 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 0.2980 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3379 Z= 0.168 Angle : 0.628 6.898 4601 Z= 0.317 Chirality : 0.045 0.150 503 Planarity : 0.004 0.036 591 Dihedral : 6.066 54.803 485 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.79 % Allowed : 21.41 % Favored : 73.80 % 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: -0.77 (0.41), residues: 417 helix: -1.50 (1.01), residues: 27 sheet: 0.11 (0.45), residues: 135 loop : -0.72 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.001 0.000 HIS A 519 PHE 0.006 0.001 PHE A 400 TYR 0.007 0.001 TYR L 94 ARG 0.006 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 75 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8576 (mmtt) cc_final: 0.8326 (tppt) REVERT: A 420 ASP cc_start: 0.8247 (m-30) cc_final: 0.7802 (m-30) REVERT: A 517 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8211 (tt) REVERT: L 39 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7525 (tm-30) outliers start: 17 outliers final: 10 residues processed: 86 average time/residue: 0.1776 time to fit residues: 18.2879 Evaluate side-chains 78 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 71 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 23 optimal weight: 0.1980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 112 GLN L 6 GLN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3379 Z= 0.181 Angle : 0.622 7.206 4601 Z= 0.310 Chirality : 0.045 0.140 503 Planarity : 0.004 0.037 591 Dihedral : 6.019 54.599 485 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.94 % Allowed : 21.41 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.41), residues: 417 helix: -1.50 (1.01), residues: 27 sheet: 0.12 (0.45), residues: 135 loop : -0.71 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.001 0.000 HIS A 519 PHE 0.006 0.001 PHE A 490 TYR 0.007 0.001 TYR A 380 ARG 0.005 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 68 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8575 (mmtt) cc_final: 0.8322 (tppt) REVERT: A 420 ASP cc_start: 0.8249 (m-30) cc_final: 0.7787 (m-30) REVERT: A 517 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8217 (tt) REVERT: H 16 GLN cc_start: 0.8591 (pm20) cc_final: 0.8254 (pm20) REVERT: H 108 ASP cc_start: 0.7739 (t0) cc_final: 0.7449 (t0) outliers start: 14 outliers final: 12 residues processed: 80 average time/residue: 0.1743 time to fit residues: 16.8893 Evaluate side-chains 78 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 71 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 24 optimal weight: 0.0050 chunk 19 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3379 Z= 0.198 Angle : 0.626 7.567 4601 Z= 0.312 Chirality : 0.045 0.141 503 Planarity : 0.004 0.038 591 Dihedral : 6.005 54.473 485 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.66 % Allowed : 21.69 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.40), residues: 417 helix: -1.50 (1.01), residues: 27 sheet: 0.41 (0.49), residues: 114 loop : -0.81 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.001 0.000 HIS A 519 PHE 0.006 0.001 PHE A 490 TYR 0.009 0.001 TYR H 104 ARG 0.006 0.001 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8548 (mmtt) cc_final: 0.8296 (tppt) REVERT: A 420 ASP cc_start: 0.8150 (m-30) cc_final: 0.7684 (m-30) REVERT: A 517 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8243 (tt) REVERT: H 3 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7640 (tm-30) REVERT: H 16 GLN cc_start: 0.8654 (pm20) cc_final: 0.8401 (pm20) REVERT: H 108 ASP cc_start: 0.7780 (t0) cc_final: 0.7506 (t0) outliers start: 13 outliers final: 12 residues processed: 76 average time/residue: 0.1765 time to fit residues: 16.0506 Evaluate side-chains 76 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 71 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 0.0870 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3379 Z= 0.181 Angle : 0.650 8.975 4601 Z= 0.321 Chirality : 0.045 0.138 503 Planarity : 0.004 0.037 591 Dihedral : 5.972 54.373 485 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.66 % Allowed : 21.97 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.40), residues: 417 helix: -1.50 (1.01), residues: 27 sheet: 0.40 (0.49), residues: 114 loop : -0.79 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.001 0.000 HIS A 519 PHE 0.006 0.001 PHE A 400 TYR 0.007 0.001 TYR A 380 ARG 0.006 0.001 ARG A 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8528 (mmtt) cc_final: 0.8288 (tppt) REVERT: A 420 ASP cc_start: 0.8145 (m-30) cc_final: 0.7675 (m-30) REVERT: A 517 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8238 (tt) REVERT: H 3 GLN cc_start: 0.8341 (tm-30) cc_final: 0.8074 (tm-30) REVERT: H 16 GLN cc_start: 0.8587 (pm20) cc_final: 0.8298 (pm20) REVERT: H 108 ASP cc_start: 0.7741 (t0) cc_final: 0.7473 (t0) outliers start: 13 outliers final: 11 residues processed: 75 average time/residue: 0.1751 time to fit residues: 15.9894 Evaluate side-chains 74 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 71 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.092734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.077205 restraints weight = 8066.260| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.46 r_work: 0.3194 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3379 Z= 0.194 Angle : 0.641 8.315 4601 Z= 0.318 Chirality : 0.045 0.135 503 Planarity : 0.004 0.037 591 Dihedral : 5.962 54.452 485 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.38 % Allowed : 22.54 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.40), residues: 417 helix: -1.49 (1.01), residues: 27 sheet: 0.32 (0.48), residues: 121 loop : -0.79 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.001 0.000 HIS A 519 PHE 0.006 0.001 PHE A 490 TYR 0.010 0.001 TYR A 380 ARG 0.007 0.001 ARG H 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1291.07 seconds wall clock time: 23 minutes 40.34 seconds (1420.34 seconds total)