Starting phenix.real_space_refine on Thu Dec 7 17:50:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctj_26992/12_2023/8ctj_26992_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctj_26992/12_2023/8ctj_26992.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctj_26992/12_2023/8ctj_26992.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctj_26992/12_2023/8ctj_26992.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctj_26992/12_2023/8ctj_26992_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctj_26992/12_2023/8ctj_26992_updated.pdb" } resolution = 4.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 18 5.16 5 C 2202 2.51 5 N 529 2.21 5 O 562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 72": "OE1" <-> "OE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 140": "OD1" <-> "OD2" Residue "A PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 254": "OD1" <-> "OD2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 434": "OD1" <-> "OD2" Residue "A GLU 437": "OE1" <-> "OE2" Residue "A PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3312 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3312 Unusual residues: {'PEE': 1} Classifications: {'peptide': 401, 'undetermined': 1} Link IDs: {'PTRANS': 10, 'TRANS': 390, None: 1} Not linked: pdbres="LEU A 474 " pdbres="PEE A 601 " Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 27 Time building chain proxies: 2.38, per 1000 atoms: 0.72 Number of scatterers: 3312 At special positions: 0 Unit cell: (55.75, 57.98, 105.925, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 1 15.00 O 562 8.00 N 529 7.00 C 2202 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 128 " distance=2.04 Simple disulfide: pdb=" SG CYS A 89 " - pdb=" SG CYS A 431 " 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 Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 637.9 milliseconds 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 12 helices and 2 sheets defined 56.6% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 91 through 94 No H-bonds generated for 'chain 'A' and resid 91 through 94' Processing helix chain 'A' and resid 98 through 110 removed outlier: 3.651A pdb=" N VAL A 101 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLU A 102 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS A 109 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A 110 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 132 removed outlier: 3.729A pdb=" N PHE A 132 " --> pdb=" O CYS A 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 128 through 132' Processing helix chain 'A' and resid 221 through 250 Proline residue: A 225 - end of helix removed outlier: 3.618A pdb=" N ILE A 228 " --> pdb=" O TYR A 224 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N CYS A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 284 Processing helix chain 'A' and resid 291 through 317 Processing helix chain 'A' and resid 328 through 352 removed outlier: 4.554A pdb=" N MET A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 392 removed outlier: 4.074A pdb=" N PHE A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE A 365 " --> pdb=" O SER A 361 " (cutoff:3.500A) Proline residue: A 366 - end of helix Processing helix chain 'A' and resid 395 through 427 removed outlier: 3.747A pdb=" N ARG A 427 " --> pdb=" O THR A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 444 through 459 Processing helix chain 'A' and resid 464 through 470 removed outlier: 4.323A pdb=" N GLN A 467 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA A 470 " --> pdb=" O GLN A 467 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 42 through 45 Processing sheet with id= B, first strand: chain 'A' and resid 52 through 59 195 hydrogen bonds defined for protein. 549 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: 0.83 Time building geometry restraints manager: 1.45 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: 977 1.34 - 1.47: 929 1.47 - 1.60: 1461 1.60 - 1.73: 1 1.73 - 1.86: 30 Bond restraints: 3398 Sorted by residual: bond pdb=" O4P PEE A 601 " pdb=" P PEE A 601 " ideal model delta sigma weight residual 1.653 1.776 -0.123 2.00e-02 2.50e+03 3.81e+01 bond pdb=" C1 PEE A 601 " pdb=" C2 PEE A 601 " ideal model delta sigma weight residual 1.519 1.555 -0.036 2.00e-02 2.50e+03 3.19e+00 bond pdb=" CA ASP A 75 " pdb=" CB ASP A 75 " ideal model delta sigma weight residual 1.531 1.577 -0.047 3.12e-02 1.03e+03 2.25e+00 bond pdb=" CB CYS A 74 " pdb=" SG CYS A 74 " ideal model delta sigma weight residual 1.808 1.855 -0.047 3.30e-02 9.18e+02 2.05e+00 bond pdb=" C2 PEE A 601 " pdb=" C3 PEE A 601 " ideal model delta sigma weight residual 1.512 1.540 -0.028 2.00e-02 2.50e+03 2.03e+00 ... (remaining 3393 not shown) Histogram of bond angle deviations from ideal: 90.91 - 99.55: 3 99.55 - 108.20: 143 108.20 - 116.84: 2156 116.84 - 125.48: 2226 125.48 - 134.13: 75 Bond angle restraints: 4603 Sorted by residual: angle pdb=" O1P PEE A 601 " pdb=" P PEE A 601 " pdb=" O2P PEE A 601 " ideal model delta sigma weight residual 119.43 133.35 -13.92 3.00e+00 1.11e-01 2.15e+01 angle pdb=" CA LYS A 213 " pdb=" CB LYS A 213 " pdb=" CG LYS A 213 " ideal model delta sigma weight residual 114.10 121.83 -7.73 2.00e+00 2.50e-01 1.49e+01 angle pdb=" N GLN A 135 " pdb=" CA GLN A 135 " pdb=" C GLN A 135 " ideal model delta sigma weight residual 110.44 106.16 4.28 1.20e+00 6.94e-01 1.27e+01 angle pdb=" CA TRP A 252 " pdb=" CB TRP A 252 " pdb=" CG TRP A 252 " ideal model delta sigma weight residual 113.60 120.05 -6.45 1.90e+00 2.77e-01 1.15e+01 angle pdb=" CA MET A 231 " pdb=" CB MET A 231 " pdb=" CG MET A 231 " ideal model delta sigma weight residual 114.10 120.85 -6.75 2.00e+00 2.50e-01 1.14e+01 ... (remaining 4598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.18: 1924 29.18 - 58.35: 50 58.35 - 87.53: 6 87.53 - 116.71: 0 116.71 - 145.89: 2 Dihedral angle restraints: 1982 sinusoidal: 805 harmonic: 1177 Sorted by residual: dihedral pdb=" CB CYS A 89 " pdb=" SG CYS A 89 " pdb=" SG CYS A 431 " pdb=" CB CYS A 431 " ideal model delta sinusoidal sigma weight residual 93.00 144.73 -51.73 1 1.00e+01 1.00e-02 3.65e+01 dihedral pdb=" O2 PEE A 601 " pdb=" C1 PEE A 601 " pdb=" C2 PEE A 601 " pdb=" O3P PEE A 601 " ideal model delta sinusoidal sigma weight residual -59.96 85.93 -145.89 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" C3 PEE A 601 " pdb=" C1 PEE A 601 " pdb=" C2 PEE A 601 " pdb=" O3P PEE A 601 " ideal model delta sinusoidal sigma weight residual 62.73 -156.57 -140.70 1 3.00e+01 1.11e-03 1.89e+01 ... (remaining 1979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 459 0.077 - 0.155: 54 0.155 - 0.232: 6 0.232 - 0.309: 0 0.309 - 0.387: 1 Chirality restraints: 520 Sorted by residual: chirality pdb=" C2 PEE A 601 " pdb=" C1 PEE A 601 " pdb=" C3 PEE A 601 " pdb=" O2 PEE A 601 " both_signs ideal model delta sigma weight residual False -2.33 -2.71 0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" CB ILE A 44 " pdb=" CA ILE A 44 " pdb=" CG1 ILE A 44 " pdb=" CG2 ILE A 44 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB THR A 405 " pdb=" CA THR A 405 " pdb=" OG1 THR A 405 " pdb=" CG2 THR A 405 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 517 not shown) Planarity restraints: 551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 371 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.62e+00 pdb=" CG ASP A 371 " -0.041 2.00e-02 2.50e+03 pdb=" OD1 ASP A 371 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP A 371 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 135 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C GLN A 135 " -0.038 2.00e-02 2.50e+03 pdb=" O GLN A 135 " 0.015 2.00e-02 2.50e+03 pdb=" N THR A 136 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 404 " -0.010 2.00e-02 2.50e+03 1.54e-02 4.17e+00 pdb=" CG PHE A 404 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 404 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 404 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 404 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 404 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 404 " 0.001 2.00e-02 2.50e+03 ... (remaining 548 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 539 2.77 - 3.30: 3286 3.30 - 3.83: 5411 3.83 - 4.37: 5971 4.37 - 4.90: 10264 Nonbonded interactions: 25471 Sorted by model distance: nonbonded pdb=" O TYR A 340 " pdb=" OG SER A 344 " model vdw 2.233 2.440 nonbonded pdb=" OG SER A 77 " pdb=" O SER A 191 " model vdw 2.233 2.440 nonbonded pdb=" O ILE A 419 " pdb=" OG1 THR A 423 " model vdw 2.276 2.440 nonbonded pdb=" O ASN A 200 " pdb=" OG SER A 203 " model vdw 2.312 2.440 nonbonded pdb=" O SER A 399 " pdb=" ND1 HIS A 403 " model vdw 2.381 2.520 ... (remaining 25466 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.240 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: 1.350 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.910 Find NCS groups from input model: 0.060 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4996 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 0.123 3398 Z= 0.316 Angle : 0.917 13.923 4603 Z= 0.487 Chirality : 0.051 0.387 520 Planarity : 0.006 0.052 551 Dihedral : 14.667 145.887 1214 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: -0.72 (0.41), residues: 395 helix: 0.26 (0.32), residues: 229 sheet: -1.55 (0.73), residues: 47 loop : -1.24 (0.56), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 244 HIS 0.001 0.000 HIS A 43 PHE 0.035 0.003 PHE A 379 TYR 0.018 0.003 TYR A 277 ARG 0.010 0.001 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1881 time to fit residues: 24.2183 Evaluate side-chains 87 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.363 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5240 ------------------------------------------------------------------------------- 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: 3.9990 chunk 30 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 135 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5356 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3398 Z= 0.205 Angle : 0.652 9.417 4603 Z= 0.338 Chirality : 0.042 0.161 520 Planarity : 0.005 0.048 551 Dihedral : 11.383 132.683 453 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % 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: 0.07 (0.42), residues: 395 helix: 0.95 (0.33), residues: 230 sheet: -1.26 (0.76), residues: 47 loop : -1.02 (0.56), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 252 HIS 0.006 0.001 HIS A 43 PHE 0.022 0.002 PHE A 276 TYR 0.013 0.002 TYR A 340 ARG 0.007 0.001 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1774 time to fit residues: 20.8870 Evaluate side-chains 79 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.331 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN A 135 GLN ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5576 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3398 Z= 0.215 Angle : 0.645 11.613 4603 Z= 0.329 Chirality : 0.041 0.137 520 Planarity : 0.005 0.035 551 Dihedral : 11.320 125.561 453 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.28 % Allowed : 6.46 % Favored : 93.26 % 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: 0.30 (0.42), residues: 395 helix: 1.22 (0.34), residues: 211 sheet: -0.89 (0.68), residues: 56 loop : -0.90 (0.56), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 177 HIS 0.009 0.003 HIS A 43 PHE 0.028 0.002 PHE A 404 TYR 0.011 0.002 TYR A 52 ARG 0.004 0.001 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 99 average time/residue: 0.1623 time to fit residues: 19.3385 Evaluate side-chains 80 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.398 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 143 HIS ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5914 moved from start: 0.8156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3398 Z= 0.321 Angle : 0.869 13.946 4603 Z= 0.442 Chirality : 0.050 0.293 520 Planarity : 0.006 0.050 551 Dihedral : 11.395 120.211 453 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 25.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % 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: -0.52 (0.41), residues: 395 helix: 0.63 (0.34), residues: 212 sheet: -1.11 (0.68), residues: 54 loop : -1.52 (0.54), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 252 HIS 0.005 0.002 HIS A 43 PHE 0.022 0.003 PHE A 276 TYR 0.027 0.003 TYR A 90 ARG 0.009 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1716 time to fit residues: 21.8050 Evaluate side-chains 85 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.363 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.0980 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 356 GLN A 394 ASN ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5916 moved from start: 0.9228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3398 Z= 0.244 Angle : 0.684 11.052 4603 Z= 0.360 Chirality : 0.044 0.158 520 Planarity : 0.005 0.041 551 Dihedral : 10.948 118.589 453 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % 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: -0.24 (0.42), residues: 395 helix: 0.80 (0.35), residues: 212 sheet: -0.70 (0.69), residues: 52 loop : -1.43 (0.54), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 252 HIS 0.007 0.002 HIS A 43 PHE 0.022 0.002 PHE A 240 TYR 0.023 0.003 TYR A 94 ARG 0.004 0.001 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1570 time to fit residues: 19.9741 Evaluate side-chains 95 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.372 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 0.3980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 356 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5884 moved from start: 0.9809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3398 Z= 0.194 Angle : 0.627 9.733 4603 Z= 0.329 Chirality : 0.042 0.142 520 Planarity : 0.004 0.041 551 Dihedral : 10.726 115.946 453 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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: 0.04 (0.42), residues: 395 helix: 1.05 (0.35), residues: 212 sheet: -0.58 (0.69), residues: 52 loop : -1.36 (0.53), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 82 HIS 0.005 0.002 HIS A 43 PHE 0.021 0.002 PHE A 240 TYR 0.017 0.002 TYR A 94 ARG 0.004 0.000 ARG A 436 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1637 time to fit residues: 20.4684 Evaluate side-chains 91 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.374 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 0.0570 chunk 15 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 135 GLN A 356 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5885 moved from start: 1.0186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3398 Z= 0.179 Angle : 0.614 10.188 4603 Z= 0.322 Chirality : 0.041 0.164 520 Planarity : 0.004 0.038 551 Dihedral : 10.522 112.419 453 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % 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: 0.25 (0.43), residues: 395 helix: 1.32 (0.36), residues: 212 sheet: -1.18 (0.63), residues: 62 loop : -1.06 (0.58), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 82 HIS 0.006 0.001 HIS A 43 PHE 0.021 0.002 PHE A 404 TYR 0.018 0.002 TYR A 94 ARG 0.002 0.000 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1554 time to fit residues: 21.0748 Evaluate side-chains 93 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.377 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 356 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5922 moved from start: 1.0752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 3398 Z= 0.194 Angle : 0.665 10.353 4603 Z= 0.349 Chirality : 0.043 0.139 520 Planarity : 0.005 0.039 551 Dihedral : 10.465 108.699 453 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % 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: 0.05 (0.42), residues: 395 helix: 0.99 (0.35), residues: 212 sheet: -1.02 (0.65), residues: 60 loop : -0.95 (0.58), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 244 HIS 0.006 0.001 HIS A 43 PHE 0.024 0.002 PHE A 404 TYR 0.023 0.002 TYR A 237 ARG 0.002 0.000 ARG A 436 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1565 time to fit residues: 21.0130 Evaluate side-chains 93 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.363 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 0.0470 chunk 3 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 0.0570 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 135 GLN A 356 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5894 moved from start: 1.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3398 Z= 0.175 Angle : 0.642 9.619 4603 Z= 0.335 Chirality : 0.042 0.139 520 Planarity : 0.004 0.038 551 Dihedral : 10.130 103.455 453 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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: 0.30 (0.43), residues: 395 helix: 1.27 (0.35), residues: 212 sheet: -0.94 (0.67), residues: 58 loop : -0.99 (0.58), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 82 HIS 0.005 0.001 HIS A 43 PHE 0.020 0.002 PHE A 404 TYR 0.023 0.002 TYR A 237 ARG 0.007 0.001 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1538 time to fit residues: 20.0423 Evaluate side-chains 98 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.375 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 31 optimal weight: 0.0570 chunk 13 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 356 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5957 moved from start: 1.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3398 Z= 0.206 Angle : 0.714 10.596 4603 Z= 0.374 Chirality : 0.043 0.200 520 Planarity : 0.004 0.037 551 Dihedral : 9.390 92.840 453 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: 0.09 (0.42), residues: 395 helix: 0.94 (0.35), residues: 212 sheet: -0.66 (0.68), residues: 55 loop : -0.97 (0.56), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 244 HIS 0.005 0.001 HIS A 43 PHE 0.026 0.002 PHE A 404 TYR 0.040 0.002 TYR A 237 ARG 0.005 0.001 ARG A 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1398 time to fit residues: 17.7751 Evaluate side-chains 91 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.369 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 3.9990 chunk 36 optimal weight: 0.2980 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 0.2980 chunk 14 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 356 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.198654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.175287 restraints weight = 6150.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.181641 restraints weight = 3701.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.185855 restraints weight = 2398.612| |-----------------------------------------------------------------------------| r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6015 moved from start: 1.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3398 Z= 0.199 Angle : 0.728 10.816 4603 Z= 0.377 Chirality : 0.043 0.204 520 Planarity : 0.004 0.040 551 Dihedral : 8.829 91.294 453 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: 0.02 (0.42), residues: 395 helix: 0.91 (0.35), residues: 212 sheet: -0.81 (0.67), residues: 55 loop : -1.00 (0.56), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 82 HIS 0.004 0.001 HIS A 43 PHE 0.029 0.002 PHE A 240 TYR 0.029 0.002 TYR A 237 ARG 0.005 0.000 ARG A 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1142.48 seconds wall clock time: 21 minutes 34.05 seconds (1294.05 seconds total)