Starting phenix.real_space_refine (version: dev) on Sun Dec 11 15:12:35 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bc6_12140/12_2022/7bc6_12140.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bc6_12140/12_2022/7bc6_12140.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bc6_12140/12_2022/7bc6_12140.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bc6_12140/12_2022/7bc6_12140.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bc6_12140/12_2022/7bc6_12140.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bc6_12140/12_2022/7bc6_12140.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.100 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 59": "NH1" <-> "NH2" Residue "A GLU 85": "OE1" <-> "OE2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A ARG 430": "NH1" <-> "NH2" Residue "B GLU 6": "OE1" <-> "OE2" Residue "B PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 99": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 4178 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3269 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 17, 'TRANS': 414} Chain: "B" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 909 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 6, 'TRANS': 110} Time building chain proxies: 2.90, per 1000 atoms: 0.69 Number of scatterers: 4178 At special positions: 0 Unit cell: (106.496, 64.896, 64.896, 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 22 16.00 O 747 8.00 N 695 7.00 C 2714 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 72 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.04 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: 1.90 Conformation dependent library (CDL) restraints added in 673.2 milliseconds 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 992 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 2 sheets defined 64.1% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 29 through 59 Proline residue: A 45 - end of helix removed outlier: 3.582A pdb=" N ARG A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 120 removed outlier: 3.989A pdb=" N THR A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU A 111 " --> pdb=" O PHE A 107 " (cutoff:3.500A) Proline residue: A 114 - end of helix removed outlier: 3.708A pdb=" N SER A 118 " --> pdb=" O PRO A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 146 Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 149 through 162 removed outlier: 4.060A pdb=" N LEU A 153 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 162 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 178 Processing helix chain 'A' and resid 184 through 207 removed outlier: 3.717A pdb=" N LEU A 192 " --> pdb=" O ARG A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.583A pdb=" N LYS A 212 " --> pdb=" O GLY A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 220 through 238 removed outlier: 3.529A pdb=" N LEU A 224 " --> pdb=" O PHE A 220 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 264 removed outlier: 3.747A pdb=" N TYR A 260 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 301 removed outlier: 3.638A pdb=" N ALA A 276 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP A 294 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 334 removed outlier: 3.566A pdb=" N ILE A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N TYR A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU A 324 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 359 Processing helix chain 'A' and resid 362 through 373 Processing helix chain 'A' and resid 374 through 378 removed outlier: 5.583A pdb=" N MET A 377 " --> pdb=" O PHE A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 389 Processing helix chain 'A' and resid 395 through 425 removed outlier: 3.549A pdb=" N PHE A 400 " --> pdb=" O GLN A 396 " (cutoff:3.500A) Proline residue: A 423 - end of helix Processing helix chain 'A' and resid 431 through 441 Processing helix chain 'A' and resid 441 through 457 removed outlier: 3.550A pdb=" N ALA A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 60 removed outlier: 3.611A pdb=" N SER B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) 260 hydrogen bonds defined for protein. 771 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.27 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 651 1.30 - 1.43: 1173 1.43 - 1.56: 2421 1.56 - 1.69: 0 1.69 - 1.81: 33 Bond restraints: 4278 Sorted by residual: bond pdb=" CA SER A 349 " pdb=" CB SER A 349 " ideal model delta sigma weight residual 1.528 1.441 0.087 1.56e-02 4.11e+03 3.12e+01 bond pdb=" CA SER A 326 " pdb=" CB SER A 326 " ideal model delta sigma weight residual 1.529 1.441 0.088 1.62e-02 3.81e+03 2.97e+01 bond pdb=" C ASN A 350 " pdb=" O ASN A 350 " ideal model delta sigma weight residual 1.237 1.175 0.062 1.17e-02 7.31e+03 2.81e+01 bond pdb=" CA SER A 325 " pdb=" CB SER A 325 " ideal model delta sigma weight residual 1.528 1.443 0.085 1.66e-02 3.63e+03 2.62e+01 bond pdb=" C ILE A 348 " pdb=" O ILE A 348 " ideal model delta sigma weight residual 1.237 1.177 0.060 1.19e-02 7.06e+03 2.52e+01 ... (remaining 4273 not shown) Histogram of bond angle deviations from ideal: 98.80 - 105.85: 88 105.85 - 112.91: 2291 112.91 - 119.96: 1510 119.96 - 127.02: 1878 127.02 - 134.08: 60 Bond angle restraints: 5827 Sorted by residual: angle pdb=" CA TYR A 296 " pdb=" C TYR A 296 " pdb=" O TYR A 296 " ideal model delta sigma weight residual 121.00 113.56 7.44 1.05e+00 9.07e-01 5.02e+01 angle pdb=" N LEU A 321 " pdb=" CA LEU A 321 " pdb=" C LEU A 321 " ideal model delta sigma weight residual 113.72 106.18 7.54 1.30e+00 5.92e-01 3.37e+01 angle pdb=" CA TYR A 296 " pdb=" C TYR A 296 " pdb=" N VAL A 297 " ideal model delta sigma weight residual 116.92 123.28 -6.36 1.16e+00 7.43e-01 3.01e+01 angle pdb=" CA VAL A 297 " pdb=" C VAL A 297 " pdb=" O VAL A 297 " ideal model delta sigma weight residual 120.95 115.55 5.40 1.04e+00 9.25e-01 2.69e+01 angle pdb=" N LEU A 327 " pdb=" CA LEU A 327 " pdb=" C LEU A 327 " ideal model delta sigma weight residual 112.38 106.17 6.21 1.22e+00 6.72e-01 2.59e+01 ... (remaining 5822 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 2254 17.69 - 35.37: 195 35.37 - 53.06: 35 53.06 - 70.74: 5 70.74 - 88.43: 2 Dihedral angle restraints: 2491 sinusoidal: 926 harmonic: 1565 Sorted by residual: dihedral pdb=" CA SER B 49 " pdb=" C SER B 49 " pdb=" N HIS B 50 " pdb=" CA HIS B 50 " ideal model delta harmonic sigma weight residual 180.00 161.83 18.17 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" N VAL A 297 " pdb=" C VAL A 297 " pdb=" CA VAL A 297 " pdb=" CB VAL A 297 " ideal model delta harmonic sigma weight residual 123.40 131.76 -8.36 0 2.50e+00 1.60e-01 1.12e+01 dihedral pdb=" CA ASN A 350 " pdb=" CB ASN A 350 " pdb=" CG ASN A 350 " pdb=" OD1 ASN A 350 " ideal model delta sinusoidal sigma weight residual 120.00 -167.54 -72.46 2 2.00e+01 2.50e-03 1.09e+01 ... (remaining 2488 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 474 0.045 - 0.091: 147 0.091 - 0.136: 36 0.136 - 0.181: 8 0.181 - 0.227: 6 Chirality restraints: 671 Sorted by residual: chirality pdb=" CA SER A 349 " pdb=" N SER A 349 " pdb=" C SER A 349 " pdb=" CB SER A 349 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA LEU A 324 " pdb=" N LEU A 324 " pdb=" C LEU A 324 " pdb=" CB LEU A 324 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA LEU A 327 " pdb=" N LEU A 327 " pdb=" C LEU A 327 " pdb=" CB LEU A 327 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 668 not shown) Planarity restraints: 728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 320 " 0.044 2.00e-02 2.50e+03 8.49e-02 7.22e+01 pdb=" C TYR A 320 " -0.147 2.00e-02 2.50e+03 pdb=" O TYR A 320 " 0.054 2.00e-02 2.50e+03 pdb=" N LEU A 321 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 349 " 0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C SER A 349 " -0.056 2.00e-02 2.50e+03 pdb=" O SER A 349 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN A 350 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 295 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C LEU A 295 " 0.055 2.00e-02 2.50e+03 pdb=" O LEU A 295 " -0.020 2.00e-02 2.50e+03 pdb=" N TYR A 296 " -0.019 2.00e-02 2.50e+03 ... (remaining 725 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 148 2.70 - 3.25: 4141 3.25 - 3.80: 6746 3.80 - 4.35: 8844 4.35 - 4.90: 15282 Nonbonded interactions: 35161 Sorted by model distance: nonbonded pdb=" NH2 ARG A 83 " pdb=" OE2 GLU B 107 " model vdw 2.145 2.520 nonbonded pdb=" NH2 ARG A 122 " pdb=" O LEU A 238 " model vdw 2.160 2.520 nonbonded pdb=" OG SER A 76 " pdb=" OE1 GLN B 39 " model vdw 2.171 2.440 nonbonded pdb=" N ALA A 26 " pdb=" O CYS A 237 " model vdw 2.211 2.520 nonbonded pdb=" OD1 ASP A 53 " pdb=" ND2 ASN A 65 " model vdw 2.214 2.520 ... (remaining 35156 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 2714 2.51 5 N 695 2.21 5 O 747 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 7.230 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.030 Process input model: 16.280 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 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 : 0.008 0.088 4278 Z= 0.491 Angle : 0.901 7.664 5827 Z= 0.559 Chirality : 0.051 0.227 671 Planarity : 0.006 0.085 728 Dihedral : 13.654 88.430 1493 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.34), residues: 545 helix: -0.07 (0.27), residues: 331 sheet: -3.73 (0.57), residues: 46 loop : -2.49 (0.45), residues: 168 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.486 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 54 average time/residue: 0.1304 time to fit residues: 9.6412 Evaluate side-chains 42 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.467 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0438 time to fit residues: 0.6597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.0980 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 4278 Z= 0.208 Angle : 0.605 7.223 5827 Z= 0.300 Chirality : 0.041 0.177 671 Planarity : 0.005 0.050 728 Dihedral : 4.421 15.014 598 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer Outliers : 1.14 % 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: -0.85 (0.36), residues: 545 helix: 0.78 (0.28), residues: 342 sheet: -3.38 (0.60), residues: 46 loop : -2.66 (0.46), residues: 157 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.470 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 47 average time/residue: 0.1195 time to fit residues: 8.0174 Evaluate side-chains 40 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.455 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0426 time to fit residues: 1.0013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.3980 chunk 15 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 135 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 4278 Z= 0.217 Angle : 0.591 6.868 5827 Z= 0.292 Chirality : 0.041 0.164 671 Planarity : 0.005 0.049 728 Dihedral : 4.254 16.575 598 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer Outliers : 0.69 % 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: -0.42 (0.36), residues: 545 helix: 1.13 (0.28), residues: 342 sheet: -3.07 (0.63), residues: 46 loop : -2.57 (0.47), residues: 157 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.472 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 37 average time/residue: 0.1118 time to fit residues: 6.1745 Evaluate side-chains 33 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.463 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0429 time to fit residues: 0.7295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.8980 chunk 36 optimal weight: 0.0000 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 4278 Z= 0.189 Angle : 0.570 6.637 5827 Z= 0.282 Chirality : 0.040 0.151 671 Planarity : 0.004 0.046 728 Dihedral : 4.072 16.346 598 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer Outliers : 1.83 % 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 (0.37), residues: 545 helix: 1.29 (0.28), residues: 349 sheet: -2.83 (0.60), residues: 56 loop : -2.20 (0.51), residues: 140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 36 time to evaluate : 0.466 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 43 average time/residue: 0.1129 time to fit residues: 7.1946 Evaluate side-chains 37 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.450 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0508 time to fit residues: 0.8925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.0070 chunk 44 optimal weight: 0.0970 chunk 36 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 135 GLN ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 4278 Z= 0.193 Angle : 0.572 7.117 5827 Z= 0.282 Chirality : 0.040 0.171 671 Planarity : 0.004 0.046 728 Dihedral : 3.977 16.894 598 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.37), residues: 545 helix: 1.48 (0.28), residues: 346 sheet: -2.64 (0.61), residues: 56 loop : -2.08 (0.51), residues: 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.482 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 41 average time/residue: 0.1104 time to fit residues: 7.0194 Evaluate side-chains 37 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.478 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0436 time to fit residues: 0.8637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 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 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 4278 Z= 0.259 Angle : 0.617 7.424 5827 Z= 0.302 Chirality : 0.042 0.169 671 Planarity : 0.004 0.045 728 Dihedral : 4.170 15.743 598 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.37), residues: 545 helix: 1.40 (0.28), residues: 342 sheet: -2.53 (0.62), residues: 56 loop : -2.37 (0.50), residues: 147 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.490 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 43 average time/residue: 0.1128 time to fit residues: 7.2522 Evaluate side-chains 37 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.465 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0452 time to fit residues: 0.8446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 4278 Z= 0.237 Angle : 0.604 7.299 5827 Z= 0.297 Chirality : 0.041 0.166 671 Planarity : 0.004 0.044 728 Dihedral : 4.131 16.221 598 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.37), residues: 545 helix: 1.48 (0.28), residues: 339 sheet: -2.46 (0.61), residues: 56 loop : -2.28 (0.49), residues: 150 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.445 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 39 average time/residue: 0.1139 time to fit residues: 6.6336 Evaluate side-chains 35 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.454 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0425 time to fit residues: 0.8418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 4278 Z= 0.231 Angle : 0.601 7.388 5827 Z= 0.296 Chirality : 0.041 0.163 671 Planarity : 0.004 0.044 728 Dihedral : 4.118 16.044 598 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.37), residues: 545 helix: 1.50 (0.28), residues: 339 sheet: -2.47 (0.60), residues: 58 loop : -2.31 (0.49), residues: 148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.462 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 38 average time/residue: 0.1129 time to fit residues: 6.4852 Evaluate side-chains 35 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.477 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0457 time to fit residues: 0.8240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 51 optimal weight: 0.0970 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 0.0970 chunk 53 optimal weight: 0.3980 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 4278 Z= 0.165 Angle : 0.557 7.515 5827 Z= 0.275 Chirality : 0.040 0.158 671 Planarity : 0.004 0.045 728 Dihedral : 3.863 16.942 598 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer Outliers : 0.23 % 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: 0.47 (0.37), residues: 545 helix: 1.70 (0.28), residues: 344 sheet: -2.12 (0.65), residues: 58 loop : -2.07 (0.50), residues: 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.489 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 39 average time/residue: 0.1116 time to fit residues: 6.5429 Evaluate side-chains 36 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.483 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0436 time to fit residues: 0.7544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.0010 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 4278 Z= 0.190 Angle : 0.577 9.533 5827 Z= 0.284 Chirality : 0.040 0.159 671 Planarity : 0.004 0.045 728 Dihedral : 3.877 16.428 598 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer Outliers : 0.23 % 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: 0.48 (0.37), residues: 545 helix: 1.77 (0.28), residues: 340 sheet: -2.12 (0.64), residues: 58 loop : -2.14 (0.49), residues: 147 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.501 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 36 average time/residue: 0.1133 time to fit residues: 6.2365 Evaluate side-chains 33 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.487 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.127158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.111660 restraints weight = 4726.439| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.65 r_work: 0.3155 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 4278 Z= 0.218 Angle : 0.593 9.265 5827 Z= 0.291 Chirality : 0.041 0.160 671 Planarity : 0.004 0.046 728 Dihedral : 3.994 16.282 598 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer Outliers : 0.23 % 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: 0.39 (0.37), residues: 545 helix: 1.68 (0.28), residues: 340 sheet: -2.12 (0.64), residues: 58 loop : -2.14 (0.50), residues: 147 =============================================================================== Job complete usr+sys time: 1201.72 seconds wall clock time: 22 minutes 27.28 seconds (1347.28 seconds total)