Starting phenix.real_space_refine on Sun Mar 10 16:00:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9k_22751/03_2024/7k9k_22751.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9k_22751/03_2024/7k9k_22751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9k_22751/03_2024/7k9k_22751.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9k_22751/03_2024/7k9k_22751.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9k_22751/03_2024/7k9k_22751.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9k_22751/03_2024/7k9k_22751.pdb" } resolution = 3.14 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= 0.071 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 12 5.16 5 C 2035 2.51 5 N 524 2.21 5 O 631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 364": "OD1" <-> "OD2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 17": "OE1" <-> "OE2" Residue "L PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 105": "OE1" <-> "OE2" 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: 3202 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1400 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 10, 'TRANS': 164} Chain breaks: 1 Chain: "H" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 947 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "L" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 806 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 100} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.28, per 1000 atoms: 0.71 Number of scatterers: 3202 At special positions: 0 Unit cell: (79.2, 63.8, 77, 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 12 16.00 O 631 8.00 N 524 7.00 C 2035 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " BETA1-6 " NAG B 1 " - " FUC B 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG B 1 " - " ASN A 343 " Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 544.2 milliseconds 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 740 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 9 sheets defined 11.7% alpha, 38.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.079A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.322A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.712A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 3.519A 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 'H' and resid 62 through 65 Processing helix chain 'L' and resid 79 through 82 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.515A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 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 6 removed outlier: 3.667A pdb=" N VAL H 18 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N CYS H 22 " --> pdb=" O ALA H 79 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 9 through 12 removed outlier: 7.133A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ILE H 34 " --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ASP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ARG H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N GLY H 44 " --> pdb=" O ARG H 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 9 through 12 removed outlier: 7.133A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYR H 109 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.631A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER L 74 " --> pdb=" O SER L 63 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER L 63 " --> pdb=" O SER L 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.817A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU L 104 " --> pdb=" O ALA L 84 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE L 33 " --> pdb=" O LYS L 49 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LYS L 49 " --> pdb=" O ILE L 33 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU L 53 " --> pdb=" O LYS L 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.817A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU L 104 " --> pdb=" O ALA L 84 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 107 hydrogen bonds defined for protein. 255 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: 0.82 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 517 1.32 - 1.45: 1013 1.45 - 1.57: 1740 1.57 - 1.70: 0 1.70 - 1.83: 14 Bond restraints: 3284 Sorted by residual: bond pdb=" C VAL A 433 " pdb=" O VAL A 433 " ideal model delta sigma weight residual 1.238 1.193 0.044 1.17e-02 7.31e+03 1.45e+01 bond pdb=" C CYS A 432 " pdb=" O CYS A 432 " ideal model delta sigma weight residual 1.235 1.198 0.038 1.14e-02 7.69e+03 1.09e+01 bond pdb=" N SER L 7 " pdb=" CA SER L 7 " ideal model delta sigma weight residual 1.456 1.489 -0.034 1.04e-02 9.25e+03 1.04e+01 bond pdb=" CA ALA A 435 " pdb=" CB ALA A 435 " ideal model delta sigma weight residual 1.535 1.482 0.053 1.90e-02 2.77e+03 7.83e+00 bond pdb=" CA SER L 7 " pdb=" CB SER L 7 " ideal model delta sigma weight residual 1.537 1.497 0.040 1.47e-02 4.63e+03 7.46e+00 ... (remaining 3279 not shown) Histogram of bond angle deviations from ideal: 101.69 - 108.18: 180 108.18 - 114.68: 1763 114.68 - 121.17: 1580 121.17 - 127.66: 913 127.66 - 134.16: 29 Bond angle restraints: 4465 Sorted by residual: angle pdb=" CA SER L 7 " pdb=" C SER L 7 " pdb=" N PRO L 8 " ideal model delta sigma weight residual 117.96 122.41 -4.45 8.10e-01 1.52e+00 3.02e+01 angle pdb=" C PRO L 15 " pdb=" CA PRO L 15 " pdb=" CB PRO L 15 " ideal model delta sigma weight residual 111.46 105.66 5.80 1.29e+00 6.01e-01 2.02e+01 angle pdb=" N GLY L 16 " pdb=" CA GLY L 16 " pdb=" C GLY L 16 " ideal model delta sigma weight residual 113.79 108.80 4.99 1.17e+00 7.31e-01 1.82e+01 angle pdb=" CA ALA L 9 " pdb=" C ALA L 9 " pdb=" O ALA L 9 " ideal model delta sigma weight residual 120.55 116.59 3.96 1.06e+00 8.90e-01 1.39e+01 angle pdb=" CA VAL A 433 " pdb=" C VAL A 433 " pdb=" O VAL A 433 " ideal model delta sigma weight residual 120.57 116.93 3.64 1.07e+00 8.73e-01 1.16e+01 ... (remaining 4460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.39: 1812 19.39 - 38.78: 120 38.78 - 58.16: 21 58.16 - 77.55: 12 77.55 - 96.94: 7 Dihedral angle restraints: 1972 sinusoidal: 807 harmonic: 1165 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual -86.00 -0.83 -85.17 1 1.00e+01 1.00e-02 8.79e+01 dihedral pdb=" CA SER L 7 " pdb=" C SER L 7 " pdb=" N PRO L 8 " pdb=" CA PRO L 8 " ideal model delta harmonic sigma weight residual 0.00 29.78 -29.78 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -41.61 -44.39 1 1.00e+01 1.00e-02 2.74e+01 ... (remaining 1969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 395 0.070 - 0.140: 83 0.140 - 0.210: 10 0.210 - 0.280: 2 0.280 - 0.350: 3 Chirality restraints: 493 Sorted by residual: chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.78 -0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CA PHE A 377 " pdb=" N PHE A 377 " pdb=" C PHE A 377 " pdb=" CB PHE A 377 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA GLN L 6 " pdb=" N GLN L 6 " pdb=" C GLN L 6 " pdb=" CB GLN L 6 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 490 not shown) Planarity restraints: 566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE L 58 " -0.036 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO L 59 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 431 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.12e+00 pdb=" C GLY A 431 " -0.035 2.00e-02 2.50e+03 pdb=" O GLY A 431 " 0.013 2.00e-02 2.50e+03 pdb=" N CYS A 432 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 98 " -0.042 9.50e-02 1.11e+02 2.49e-02 3.50e+00 pdb=" NE ARG H 98 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG H 98 " -0.031 2.00e-02 2.50e+03 pdb=" NH1 ARG H 98 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG H 98 " 0.009 2.00e-02 2.50e+03 ... (remaining 563 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 217 2.73 - 3.27: 3220 3.27 - 3.82: 4945 3.82 - 4.36: 6169 4.36 - 4.90: 10675 Nonbonded interactions: 25226 Sorted by model distance: nonbonded pdb=" OG SER H 17 " pdb=" O LEU H 83 " model vdw 2.188 2.440 nonbonded pdb=" O PHE H 107 " pdb=" NE1 TRP H 110 " model vdw 2.232 2.520 nonbonded pdb=" OG SER H 66 " pdb=" OE1 GLU H 67 " model vdw 2.243 2.440 nonbonded pdb=" N LEU A 455 " pdb=" O PRO A 491 " model vdw 2.270 2.520 nonbonded pdb=" OD1 ASN A 439 " pdb=" OG SER A 443 " model vdw 2.301 2.440 ... (remaining 25221 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: 1.140 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: 5.700 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.370 Find NCS groups from input model: 0.090 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 3284 Z= 0.410 Angle : 0.960 6.979 4465 Z= 0.556 Chirality : 0.063 0.350 493 Planarity : 0.005 0.055 565 Dihedral : 15.505 96.937 1217 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.39), residues: 394 helix: -1.50 (0.85), residues: 34 sheet: -0.41 (0.41), residues: 129 loop : -1.06 (0.39), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 436 HIS 0.005 0.003 HIS L 34 PHE 0.026 0.002 PHE A 497 TYR 0.028 0.003 TYR H 80 ARG 0.031 0.003 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 442 ASP cc_start: 0.7791 (m-30) cc_final: 0.7456 (m-30) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1522 time to fit residues: 14.8733 Evaluate side-chains 63 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 5.9990 chunk 29 optimal weight: 0.1980 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 15 optimal weight: 0.6980 chunk 30 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 0.0970 chunk 22 optimal weight: 6.9990 chunk 35 optimal weight: 0.0770 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3284 Z= 0.164 Angle : 0.670 9.501 4465 Z= 0.339 Chirality : 0.046 0.170 493 Planarity : 0.005 0.049 565 Dihedral : 8.991 56.801 521 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.02 % Allowed : 9.25 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.94 (0.42), residues: 394 helix: -1.40 (1.08), residues: 28 sheet: -0.16 (0.40), residues: 146 loop : -0.79 (0.42), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 99 HIS 0.002 0.001 HIS A 519 PHE 0.012 0.001 PHE A 377 TYR 0.015 0.001 TYR A 421 ARG 0.005 0.001 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 0.358 Fit side-chains REVERT: A 406 GLU cc_start: 0.7603 (mp0) cc_final: 0.7073 (mp0) REVERT: A 442 ASP cc_start: 0.7707 (m-30) cc_final: 0.7317 (m-30) REVERT: L 105 GLU cc_start: 0.5916 (tp30) cc_final: 0.5697 (tp30) outliers start: 7 outliers final: 2 residues processed: 74 average time/residue: 0.1585 time to fit residues: 14.3004 Evaluate side-chains 67 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 40 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3284 Z= 0.345 Angle : 0.733 13.903 4465 Z= 0.358 Chirality : 0.047 0.174 493 Planarity : 0.005 0.049 565 Dihedral : 7.526 55.548 521 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.47 % Allowed : 13.01 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 (0.41), residues: 394 helix: -1.87 (1.01), residues: 28 sheet: 0.28 (0.42), residues: 146 loop : -0.94 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 436 HIS 0.003 0.002 HIS L 34 PHE 0.017 0.002 PHE A 497 TYR 0.020 0.002 TYR H 102 ARG 0.003 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 0.373 Fit side-chains REVERT: A 403 ARG cc_start: 0.7570 (ptm160) cc_final: 0.7137 (ptm-80) REVERT: A 406 GLU cc_start: 0.7796 (mp0) cc_final: 0.7377 (mp0) REVERT: A 442 ASP cc_start: 0.7649 (m-30) cc_final: 0.7249 (m-30) REVERT: H 112 GLN cc_start: 0.7050 (OUTLIER) cc_final: 0.6656 (mp10) REVERT: L 105 GLU cc_start: 0.5342 (tp30) cc_final: 0.5091 (tp30) outliers start: 12 outliers final: 9 residues processed: 72 average time/residue: 0.1515 time to fit residues: 13.3873 Evaluate side-chains 75 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 40 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 0.3980 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3284 Z= 0.239 Angle : 0.657 12.801 4465 Z= 0.321 Chirality : 0.045 0.161 493 Planarity : 0.005 0.052 565 Dihedral : 6.913 54.107 521 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.76 % Allowed : 13.29 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 (0.42), residues: 394 helix: -2.23 (0.84), residues: 34 sheet: 0.44 (0.42), residues: 145 loop : -0.85 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS L 34 PHE 0.012 0.002 PHE A 497 TYR 0.020 0.002 TYR H 80 ARG 0.003 0.001 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 0.365 Fit side-chains REVERT: A 403 ARG cc_start: 0.7585 (ptm160) cc_final: 0.7012 (ptm-80) REVERT: A 406 GLU cc_start: 0.7789 (mp0) cc_final: 0.7237 (mp0) REVERT: A 442 ASP cc_start: 0.7642 (m-30) cc_final: 0.7209 (m-30) REVERT: H 112 GLN cc_start: 0.7069 (OUTLIER) cc_final: 0.6706 (mp10) REVERT: L 105 GLU cc_start: 0.5300 (tp30) cc_final: 0.5049 (tp30) outliers start: 13 outliers final: 8 residues processed: 72 average time/residue: 0.1488 time to fit residues: 13.1559 Evaluate side-chains 73 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 40 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 3284 Z= 0.407 Angle : 0.729 9.788 4465 Z= 0.365 Chirality : 0.047 0.162 493 Planarity : 0.005 0.054 565 Dihedral : 7.121 50.929 521 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.34 % Allowed : 14.74 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.41), residues: 394 helix: -2.62 (0.78), residues: 34 sheet: 0.23 (0.43), residues: 146 loop : -0.99 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 47 HIS 0.004 0.002 HIS L 34 PHE 0.014 0.002 PHE A 497 TYR 0.020 0.002 TYR H 102 ARG 0.003 0.001 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 64 time to evaluate : 0.366 Fit side-chains REVERT: A 403 ARG cc_start: 0.7838 (ptm160) cc_final: 0.7405 (ptm-80) REVERT: A 442 ASP cc_start: 0.7611 (m-30) cc_final: 0.7177 (m-30) REVERT: H 112 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6729 (mp10) outliers start: 15 outliers final: 11 residues processed: 71 average time/residue: 0.1473 time to fit residues: 12.8835 Evaluate side-chains 77 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 78 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3284 Z= 0.244 Angle : 0.657 9.656 4465 Z= 0.327 Chirality : 0.044 0.152 493 Planarity : 0.005 0.055 565 Dihedral : 6.745 48.676 521 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.05 % Allowed : 16.18 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 (0.42), residues: 394 helix: -2.56 (0.73), residues: 40 sheet: 0.18 (0.42), residues: 151 loop : -0.81 (0.44), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.003 0.001 HIS L 34 PHE 0.010 0.001 PHE A 497 TYR 0.018 0.002 TYR H 80 ARG 0.003 0.001 ARG H 65 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 68 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 442 ASP cc_start: 0.7555 (m-30) cc_final: 0.7117 (m-30) REVERT: H 112 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.6803 (mp10) REVERT: L 105 GLU cc_start: 0.5624 (tp30) cc_final: 0.5372 (tp30) outliers start: 14 outliers final: 9 residues processed: 72 average time/residue: 0.1507 time to fit residues: 13.2999 Evaluate side-chains 73 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 69 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3284 Z= 0.319 Angle : 0.683 8.582 4465 Z= 0.343 Chirality : 0.045 0.163 493 Planarity : 0.005 0.057 565 Dihedral : 6.720 44.986 521 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.76 % Allowed : 17.92 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.43), residues: 394 helix: -2.57 (0.74), residues: 40 sheet: 0.02 (0.42), residues: 159 loop : -0.84 (0.46), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 47 HIS 0.003 0.001 HIS L 34 PHE 0.011 0.002 PHE L 71 TYR 0.016 0.002 TYR A 369 ARG 0.003 0.001 ARG H 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.388 Fit side-chains REVERT: A 403 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7489 (ptm-80) REVERT: A 442 ASP cc_start: 0.7559 (m-30) cc_final: 0.7112 (m-30) REVERT: H 112 GLN cc_start: 0.7090 (OUTLIER) cc_final: 0.6711 (mp10) REVERT: L 105 GLU cc_start: 0.5734 (tp30) cc_final: 0.5363 (tp30) outliers start: 13 outliers final: 9 residues processed: 67 average time/residue: 0.1461 time to fit residues: 12.1481 Evaluate side-chains 75 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 78 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 0.1980 chunk 34 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 15 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3284 Z= 0.198 Angle : 0.633 8.889 4465 Z= 0.316 Chirality : 0.044 0.182 493 Planarity : 0.005 0.059 565 Dihedral : 6.304 42.304 521 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.34 % Allowed : 17.92 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.98 (0.43), residues: 394 helix: -2.71 (0.72), residues: 41 sheet: 0.09 (0.42), residues: 159 loop : -0.72 (0.46), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.002 0.001 HIS L 34 PHE 0.009 0.001 PHE L 71 TYR 0.015 0.001 TYR H 80 ARG 0.004 0.000 ARG H 65 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 68 time to evaluate : 0.335 Fit side-chains REVERT: A 403 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7482 (ptm-80) REVERT: A 442 ASP cc_start: 0.7510 (m-30) cc_final: 0.7068 (m-30) REVERT: H 112 GLN cc_start: 0.7059 (OUTLIER) cc_final: 0.6668 (mp10) REVERT: L 105 GLU cc_start: 0.5350 (tp30) cc_final: 0.5012 (tp30) outliers start: 15 outliers final: 11 residues processed: 73 average time/residue: 0.1453 time to fit residues: 13.0473 Evaluate side-chains 76 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 41 ASN Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 106 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.2980 chunk 34 optimal weight: 0.5980 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 17 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3284 Z= 0.201 Angle : 0.639 8.459 4465 Z= 0.321 Chirality : 0.045 0.189 493 Planarity : 0.005 0.058 565 Dihedral : 6.104 41.825 521 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.05 % Allowed : 18.79 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.94 (0.43), residues: 394 helix: -2.71 (0.72), residues: 41 sheet: 0.13 (0.42), residues: 159 loop : -0.71 (0.46), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.002 0.001 HIS L 34 PHE 0.009 0.001 PHE L 71 TYR 0.014 0.001 TYR A 369 ARG 0.004 0.000 ARG L 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 442 ASP cc_start: 0.7501 (m-30) cc_final: 0.7054 (m-30) REVERT: H 112 GLN cc_start: 0.7048 (OUTLIER) cc_final: 0.6663 (mp10) outliers start: 14 outliers final: 10 residues processed: 68 average time/residue: 0.1505 time to fit residues: 12.5425 Evaluate side-chains 74 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 63 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 78 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 24 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 4 optimal weight: 0.0980 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 0.0870 chunk 12 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 3284 Z= 0.169 Angle : 0.670 11.862 4465 Z= 0.330 Chirality : 0.046 0.270 493 Planarity : 0.005 0.057 565 Dihedral : 5.667 41.273 521 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.47 % Allowed : 19.94 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.72 (0.43), residues: 394 helix: -2.70 (0.72), residues: 40 sheet: 0.42 (0.42), residues: 158 loop : -0.67 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.001 0.000 HIS L 34 PHE 0.007 0.001 PHE A 377 TYR 0.012 0.001 TYR A 369 ARG 0.004 0.000 ARG H 65 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 0.336 Fit side-chains REVERT: A 403 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7448 (ptm-80) REVERT: A 442 ASP cc_start: 0.7515 (m-30) cc_final: 0.7038 (m-30) REVERT: H 112 GLN cc_start: 0.7003 (OUTLIER) cc_final: 0.6633 (mp10) outliers start: 12 outliers final: 8 residues processed: 73 average time/residue: 0.1643 time to fit residues: 14.5280 Evaluate side-chains 78 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 41 ASN Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 106 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 22 optimal weight: 0.0980 chunk 35 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 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 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.132060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.110633 restraints weight = 5954.836| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 3.18 r_work: 0.3457 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 3284 Z= 0.193 Angle : 0.678 14.246 4465 Z= 0.339 Chirality : 0.045 0.224 493 Planarity : 0.005 0.058 565 Dihedral : 5.644 40.778 521 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.18 % Allowed : 19.65 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.74 (0.43), residues: 394 helix: -2.76 (0.70), residues: 40 sheet: 0.36 (0.42), residues: 159 loop : -0.64 (0.46), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.001 0.001 HIS L 34 PHE 0.008 0.001 PHE L 71 TYR 0.018 0.001 TYR H 80 ARG 0.004 0.000 ARG H 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1184.57 seconds wall clock time: 22 minutes 12.89 seconds (1332.89 seconds total)