Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 13:25:56 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m7d_30129/12_2021/6m7d_30129.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m7d_30129/12_2021/6m7d_30129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m7d_30129/12_2021/6m7d_30129.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m7d_30129/12_2021/6m7d_30129.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m7d_30129/12_2021/6m7d_30129.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m7d_30129/12_2021/6m7d_30129.pdb" } resolution = 2.9 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= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model 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 None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 3280 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3160 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 15, 'TRANS': 396} Chain: "B" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'RNA': 6} Modifications used: {'rna3p_pyr': 5, 'rna2p_pyr': 1} Link IDs: {'rna3p': 4, 'rna2p': 1} Time building chain proxies: 2.40, per 1000 atoms: 0.73 Number of scatterers: 3280 At special positions: 0 Unit cell: (78.52, 81.64, 88.4, 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 14 16.00 P 6 15.00 O 654 8.00 N 552 7.00 C 2054 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amimo 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: 1.41 Conformation dependent library (CDL) restraints added in 491.5 milliseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 752 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 1 sheets defined 67.5% alpha, 5.3% beta 0 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 5 through 10 Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 46 through 63 Processing helix chain 'A' and resid 67 through 81 Processing helix chain 'A' and resid 85 through 94 Processing helix chain 'A' and resid 128 through 136 Processing helix chain 'A' and resid 153 through 161 Processing helix chain 'A' and resid 162 through 182 removed outlier: 4.144A pdb=" N LYS A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 203 removed outlier: 4.224A pdb=" N ALA A 198 " --> pdb=" O ASN A 194 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.763A pdb=" N VAL A 210 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 226 Processing helix chain 'A' and resid 226 through 240 Processing helix chain 'A' and resid 248 through 262 Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 289 through 306 Processing helix chain 'A' and resid 307 through 313 Proline residue: A 311 - end of helix Processing helix chain 'A' and resid 318 through 328 removed outlier: 4.001A pdb=" N GLY A 322 " --> pdb=" O PRO A 319 " (cutoff:3.500A) Proline residue: A 326 - end of helix Processing helix chain 'A' and resid 329 through 344 Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 358 through 371 Processing helix chain 'A' and resid 380 through 385 Processing helix chain 'A' and resid 387 through 402 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 40 removed outlier: 6.533A pdb=" N SER A 33 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL A 102 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL A 35 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYR A 104 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL A 37 " --> pdb=" O TYR A 104 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE A 106 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL A 39 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N LYS A 108 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN A 105 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A 120 " --> pdb=" O TYR A 127 " (cutoff:3.500A) 185 hydrogen bonds defined for protein. 516 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 4 stacking parallelities Total time for adding SS restraints: 0.93 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 683 1.33 - 1.45: 765 1.45 - 1.57: 1863 1.57 - 1.69: 11 1.69 - 1.81: 26 Bond restraints: 3348 Sorted by residual: bond pdb=" N SER A 142 " pdb=" CA SER A 142 " ideal model delta sigma weight residual 1.453 1.488 -0.034 9.20e-03 1.18e+04 1.39e+01 bond pdb=" N VAL A 277 " pdb=" CA VAL A 277 " ideal model delta sigma weight residual 1.452 1.496 -0.044 1.18e-02 7.18e+03 1.37e+01 bond pdb=" N VAL A 99 " pdb=" CA VAL A 99 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.08e-02 8.57e+03 1.24e+01 bond pdb=" N VAL A 95 " pdb=" CA VAL A 95 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.10e-02 8.26e+03 9.85e+00 bond pdb=" N MET A 125 " pdb=" CA MET A 125 " ideal model delta sigma weight residual 1.456 1.491 -0.036 1.22e-02 6.72e+03 8.47e+00 ... (remaining 3343 not shown) Histogram of bond angle deviations from ideal: 99.56 - 106.45: 105 106.45 - 113.33: 1851 113.33 - 120.22: 1305 120.22 - 127.10: 1271 127.10 - 133.98: 24 Bond angle restraints: 4556 Sorted by residual: angle pdb=" CA ASP A 405 " pdb=" C ASP A 405 " pdb=" O ASP A 405 " ideal model delta sigma weight residual 122.63 118.22 4.41 1.29e+00 6.01e-01 1.17e+01 angle pdb=" N THR A 272 " pdb=" CA THR A 272 " pdb=" C THR A 272 " ideal model delta sigma weight residual 111.28 107.63 3.65 1.09e+00 8.42e-01 1.12e+01 angle pdb=" C ASN A 241 " pdb=" N THR A 242 " pdb=" CA THR A 242 " ideal model delta sigma weight residual 120.28 124.74 -4.46 1.34e+00 5.57e-01 1.11e+01 angle pdb=" C SER A 402 " pdb=" N GLY A 403 " pdb=" CA GLY A 403 " ideal model delta sigma weight residual 120.00 123.63 -3.63 1.10e+00 8.26e-01 1.09e+01 angle pdb=" CA ARG A 149 " pdb=" C ARG A 149 " pdb=" O ARG A 149 " ideal model delta sigma weight residual 121.56 118.10 3.46 1.09e+00 8.42e-01 1.01e+01 ... (remaining 4551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 1807 17.82 - 35.64: 155 35.64 - 53.46: 30 53.46 - 71.28: 6 71.28 - 89.10: 3 Dihedral angle restraints: 2001 sinusoidal: 823 harmonic: 1178 Sorted by residual: dihedral pdb=" C GLU A 278 " pdb=" N GLU A 278 " pdb=" CA GLU A 278 " pdb=" CB GLU A 278 " ideal model delta harmonic sigma weight residual -122.60 -130.72 8.12 0 2.50e+00 1.60e-01 1.06e+01 dihedral pdb=" CA ASN A 140 " pdb=" CB ASN A 140 " pdb=" CG ASN A 140 " pdb=" OD1 ASN A 140 " ideal model delta sinusoidal sigma weight residual -90.00 -159.31 69.31 2 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" CB GLU A 214 " pdb=" CG GLU A 214 " pdb=" CD GLU A 214 " pdb=" OE1 GLU A 214 " ideal model delta sinusoidal sigma weight residual 0.00 89.10 -89.10 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 1998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 286 0.046 - 0.092: 152 0.092 - 0.139: 69 0.139 - 0.185: 17 0.185 - 0.231: 9 Chirality restraints: 533 Sorted by residual: chirality pdb=" CA GLU A 278 " pdb=" N GLU A 278 " pdb=" C GLU A 278 " pdb=" CB GLU A 278 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA VAL A 120 " pdb=" N VAL A 120 " pdb=" C VAL A 120 " pdb=" CB VAL A 120 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE A 273 " pdb=" N ILE A 273 " pdb=" C ILE A 273 " pdb=" CB ILE A 273 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 530 not shown) Planarity restraints: 564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U B 2 " 0.031 2.00e-02 2.50e+03 1.53e-02 5.25e+00 pdb=" N1 U B 2 " -0.031 2.00e-02 2.50e+03 pdb=" C2 U B 2 " -0.007 2.00e-02 2.50e+03 pdb=" O2 U B 2 " -0.003 2.00e-02 2.50e+03 pdb=" N3 U B 2 " 0.005 2.00e-02 2.50e+03 pdb=" C4 U B 2 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U B 2 " 0.009 2.00e-02 2.50e+03 pdb=" C5 U B 2 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U B 2 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 240 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C MET A 240 " 0.033 2.00e-02 2.50e+03 pdb=" O MET A 240 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN A 241 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 44 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C VAL A 44 " -0.031 2.00e-02 2.50e+03 pdb=" O VAL A 44 " 0.012 2.00e-02 2.50e+03 pdb=" N THR A 45 " 0.010 2.00e-02 2.50e+03 ... (remaining 561 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 115 2.71 - 3.25: 3405 3.25 - 3.80: 5504 3.80 - 4.35: 7360 4.35 - 4.90: 11397 Nonbonded interactions: 27781 Sorted by model distance: nonbonded pdb=" O ALA A 346 " pdb=" O2' U B 4 " model vdw 2.157 2.440 nonbonded pdb=" O THR A 183 " pdb=" O2' U B 2 " model vdw 2.198 2.440 nonbonded pdb=" O ALA A 325 " pdb=" ND2 ASN A 328 " model vdw 2.211 2.520 nonbonded pdb=" NE2 GLN A 173 " pdb=" O LEU A 209 " model vdw 2.220 2.520 nonbonded pdb=" OD2 ASP A 202 " pdb=" OG1 THR A 204 " model vdw 2.262 2.440 ... (remaining 27776 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 14 5.16 5 C 2054 2.51 5 N 552 2.21 5 O 654 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 Write .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: 5.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 26.510 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.050 Process input model: 16.740 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:10.140 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 59.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 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 : 0.010 0.056 3348 Z= 0.657 Angle : 1.033 5.361 4556 Z= 0.761 Chirality : 0.069 0.231 533 Planarity : 0.005 0.041 564 Dihedral : 13.842 89.104 1249 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 0.58 % 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: -0.46 (0.38), residues: 410 helix: -0.14 (0.32), residues: 244 sheet: -0.49 (1.15), residues: 23 loop : -0.28 (0.41), residues: 143 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 0.411 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 68 average time/residue: 1.2779 time to fit residues: 89.3079 Evaluate side-chains 48 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.394 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.5357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN A 93 ASN A 140 ASN A 227 GLN A 241 ASN ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN A 288 ASN A 366 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 3348 Z= 0.162 Angle : 0.475 4.717 4556 Z= 0.258 Chirality : 0.040 0.152 533 Planarity : 0.004 0.032 564 Dihedral : 4.830 24.955 515 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer Outliers : 2.92 % 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: 1.02 (0.39), residues: 410 helix: 0.95 (0.33), residues: 241 sheet: -0.04 (1.02), residues: 23 loop : 0.59 (0.45), residues: 146 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 0.401 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 57 average time/residue: 1.1017 time to fit residues: 64.9338 Evaluate side-chains 49 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.384 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.1693 time to fit residues: 0.9092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 10.0000 chunk 11 optimal weight: 30.0000 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 ASN A 348 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 3348 Z= 0.273 Angle : 0.505 4.904 4556 Z= 0.270 Chirality : 0.042 0.144 533 Planarity : 0.004 0.031 564 Dihedral : 4.893 24.079 515 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 4.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.40), residues: 410 helix: 1.05 (0.33), residues: 239 sheet: 0.25 (0.98), residues: 25 loop : 0.88 (0.48), residues: 146 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 43 time to evaluate : 0.359 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 52 average time/residue: 1.1163 time to fit residues: 60.0569 Evaluate side-chains 46 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.380 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 1.0915 time to fit residues: 2.7475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN A 328 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 3348 Z= 0.143 Angle : 0.444 4.905 4556 Z= 0.237 Chirality : 0.039 0.134 533 Planarity : 0.003 0.033 564 Dihedral : 4.731 27.229 515 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer Outliers : 3.79 % 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: 1.73 (0.41), residues: 410 helix: 1.38 (0.34), residues: 243 sheet: 0.52 (0.93), residues: 25 loop : 1.13 (0.51), residues: 142 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 42 time to evaluate : 0.355 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 50 average time/residue: 1.1163 time to fit residues: 57.6924 Evaluate side-chains 47 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.401 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 1.7285 time to fit residues: 2.2630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 ASN A 348 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 3348 Z= 0.228 Angle : 0.478 5.466 4556 Z= 0.253 Chirality : 0.041 0.127 533 Planarity : 0.003 0.034 564 Dihedral : 4.810 27.181 515 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 3.21 % 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: 1.79 (0.41), residues: 410 helix: 1.37 (0.34), residues: 240 sheet: 0.67 (0.90), residues: 25 loop : 1.25 (0.51), residues: 145 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 0.385 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 47 average time/residue: 1.0867 time to fit residues: 52.9243 Evaluate side-chains 44 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.364 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.5001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 0.2980 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 3348 Z= 0.135 Angle : 0.462 8.789 4556 Z= 0.236 Chirality : 0.039 0.125 533 Planarity : 0.003 0.030 564 Dihedral : 4.691 28.854 515 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer Outliers : 2.92 % 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: 2.03 (0.41), residues: 410 helix: 1.62 (0.34), residues: 242 sheet: 0.84 (0.90), residues: 25 loop : 1.22 (0.51), residues: 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 0.382 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 50 average time/residue: 1.0370 time to fit residues: 53.7817 Evaluate side-chains 44 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.394 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 0.5310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 24 optimal weight: 0.0570 chunk 18 optimal weight: 0.3980 chunk 15 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 20.0000 chunk 7 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.6500 ------------------------------------------------------------------------------- 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: 0.8483 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 3348 Z= 0.129 Angle : 0.450 7.369 4556 Z= 0.231 Chirality : 0.039 0.150 533 Planarity : 0.003 0.031 564 Dihedral : 4.656 30.955 515 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer Outliers : 2.92 % 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: 2.21 (0.42), residues: 410 helix: 1.79 (0.34), residues: 242 sheet: 0.91 (0.93), residues: 25 loop : 1.23 (0.52), residues: 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 0.387 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 55 average time/residue: 0.8972 time to fit residues: 51.3757 Evaluate side-chains 47 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.358 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.6598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 31 optimal weight: 0.1980 chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 34 optimal weight: 0.0040 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 3348 Z= 0.128 Angle : 0.455 6.585 4556 Z= 0.235 Chirality : 0.039 0.152 533 Planarity : 0.003 0.032 564 Dihedral : 4.622 31.803 515 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 1.75 % 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: 2.26 (0.42), residues: 410 helix: 1.82 (0.34), residues: 243 sheet: 0.84 (0.93), residues: 25 loop : 1.28 (0.53), residues: 142 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.375 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 49 average time/residue: 1.0589 time to fit residues: 53.7709 Evaluate side-chains 47 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.384 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.5213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 3348 Z= 0.318 Angle : 0.548 6.631 4556 Z= 0.283 Chirality : 0.044 0.171 533 Planarity : 0.004 0.031 564 Dihedral : 4.956 34.711 515 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 2.92 % 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: 1.82 (0.41), residues: 410 helix: 1.40 (0.34), residues: 239 sheet: 0.65 (0.89), residues: 25 loop : 1.26 (0.52), residues: 146 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 45 time to evaluate : 0.361 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 54 average time/residue: 1.0898 time to fit residues: 60.8039 Evaluate side-chains 46 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.396 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.5449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.1980 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 29 optimal weight: 0.0870 chunk 4 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 3348 Z= 0.141 Angle : 0.471 6.848 4556 Z= 0.245 Chirality : 0.039 0.141 533 Planarity : 0.003 0.032 564 Dihedral : 4.701 28.639 515 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 2.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.41), residues: 410 helix: 1.62 (0.34), residues: 242 sheet: 0.80 (0.91), residues: 25 loop : 1.28 (0.52), residues: 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 0.388 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 48 average time/residue: 0.9940 time to fit residues: 49.6789 Evaluate side-chains 46 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.375 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 0.5221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 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 = 0.3580 r_free = 0.3580 target = 0.153863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.133482 restraints weight = 3390.488| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.19 r_work: 0.3266 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 2.02 restraints_weight: 0.2500 r_work: 0.3069 rms_B_bonded: 3.70 restraints_weight: 0.1250 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 3348 Z= 0.160 Angle : 0.483 6.850 4556 Z= 0.249 Chirality : 0.040 0.181 533 Planarity : 0.003 0.033 564 Dihedral : 4.668 28.997 515 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 1.46 % 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: 2.10 (0.41), residues: 410 helix: 1.66 (0.34), residues: 241 sheet: 0.80 (0.91), residues: 25 loop : 1.31 (0.52), residues: 144 =============================================================================== Job complete usr+sys time: 1877.53 seconds wall clock time: 34 minutes 58.53 seconds (2098.53 seconds total)