Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 13:31:04 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zpg_11338/12_2021/6zpg_11338.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zpg_11338/12_2021/6zpg_11338.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zpg_11338/12_2021/6zpg_11338.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zpg_11338/12_2021/6zpg_11338.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zpg_11338/12_2021/6zpg_11338.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zpg_11338/12_2021/6zpg_11338.pdb" } resolution = 4.6 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= 0.003 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: 3808 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3808 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 12, 'CIS': 1, 'TRANS': 449} Chain breaks: 8 Time building chain proxies: 2.39, per 1000 atoms: 0.63 Number of scatterers: 3808 At special positions: 0 Unit cell: (90.741, 124.117, 65.709, 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 24 16.00 O 687 8.00 N 657 7.00 C 2440 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: 1.44 Conformation dependent library (CDL) restraints added in 631.8 milliseconds 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 904 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 85.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 5 through 24 Processing helix chain 'A' and resid 34 through 51 removed outlier: 4.245A pdb=" N GLY A 51 " --> pdb=" O LYS A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 109 removed outlier: 3.739A pdb=" N ALA A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 128 Processing helix chain 'A' and resid 135 through 153 removed outlier: 3.723A pdb=" N GLU A 153 " --> pdb=" O TRP A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 175 Processing helix chain 'A' and resid 200 through 221 Processing helix chain 'A' and resid 223 through 240 Processing helix chain 'A' and resid 249 through 263 Processing helix chain 'A' and resid 266 through 282 Processing helix chain 'A' and resid 305 through 330 Processing helix chain 'A' and resid 393 through 413 Processing helix chain 'A' and resid 416 through 433 Processing helix chain 'A' and resid 437 through 455 removed outlier: 4.011A pdb=" N GLU A 441 " --> pdb=" O GLU A 437 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 443 " --> pdb=" O ASP A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' Processing helix chain 'A' and resid 463 through 495 Processing helix chain 'A' and resid 499 through 523 Processing helix chain 'A' and resid 540 through 557 removed outlier: 3.561A pdb=" N MET A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 584 Processing helix chain 'A' and resid 589 through 607 309 hydrogen bonds defined for protein. 927 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.95 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1229 1.34 - 1.46: 771 1.46 - 1.58: 1844 1.58 - 1.70: 0 1.70 - 1.81: 37 Bond restraints: 3881 Sorted by residual: bond pdb=" C ARG A 541 " pdb=" N PRO A 542 " ideal model delta sigma weight residual 1.336 1.395 -0.059 1.23e-02 6.61e+03 2.34e+01 bond pdb=" N GLU A 175 " pdb=" CA GLU A 175 " ideal model delta sigma weight residual 1.457 1.485 -0.027 1.29e-02 6.01e+03 4.50e+00 bond pdb=" C ASP A 497 " pdb=" N PRO A 498 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.21e+00 bond pdb=" C ASP A 526 " pdb=" N PRO A 527 " ideal model delta sigma weight residual 1.341 1.361 -0.020 1.60e-02 3.91e+03 1.61e+00 bond pdb=" CB GLN A 282 " pdb=" CG GLN A 282 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.59e+00 ... (remaining 3876 not shown) Histogram of bond angle deviations from ideal: 97.85 - 105.51: 53 105.51 - 113.17: 2081 113.17 - 120.83: 2038 120.83 - 128.49: 1016 128.49 - 136.15: 34 Bond angle restraints: 5222 Sorted by residual: angle pdb=" C GLU A 222 " pdb=" N MET A 223 " pdb=" CA MET A 223 " ideal model delta sigma weight residual 121.54 129.03 -7.49 1.91e+00 2.74e-01 1.54e+01 angle pdb=" C GLU A 175 " pdb=" N VAL A 176 " pdb=" CA VAL A 176 " ideal model delta sigma weight residual 121.70 127.98 -6.28 1.80e+00 3.09e-01 1.22e+01 angle pdb=" C HIS A 304 " pdb=" N GLN A 305 " pdb=" CA GLN A 305 " ideal model delta sigma weight residual 121.54 127.74 -6.20 1.91e+00 2.74e-01 1.05e+01 angle pdb=" N LEU A 607 " pdb=" CA LEU A 607 " pdb=" C LEU A 607 " ideal model delta sigma weight residual 109.81 116.98 -7.17 2.21e+00 2.05e-01 1.05e+01 angle pdb=" C LYS A 174 " pdb=" N GLU A 175 " pdb=" CA GLU A 175 " ideal model delta sigma weight residual 121.54 127.59 -6.05 1.91e+00 2.74e-01 1.00e+01 ... (remaining 5217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.79: 2027 15.79 - 31.58: 248 31.58 - 47.37: 69 47.37 - 63.15: 13 63.15 - 78.94: 8 Dihedral angle restraints: 2365 sinusoidal: 982 harmonic: 1383 Sorted by residual: dihedral pdb=" CA MET A 223 " pdb=" C MET A 223 " pdb=" N PHE A 224 " pdb=" CA PHE A 224 " ideal model delta harmonic sigma weight residual -180.00 -154.83 -25.17 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA GLY A 555 " pdb=" C GLY A 555 " pdb=" N LYS A 556 " pdb=" CA LYS A 556 " ideal model delta harmonic sigma weight residual -180.00 -160.91 -19.09 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA ASP A 561 " pdb=" C ASP A 561 " pdb=" N PRO A 562 " pdb=" CA PRO A 562 " ideal model delta harmonic sigma weight residual 180.00 -161.76 -18.24 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 2362 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 444 0.056 - 0.111: 103 0.111 - 0.167: 23 0.167 - 0.222: 4 0.222 - 0.278: 1 Chirality restraints: 575 Sorted by residual: chirality pdb=" CB ILE A 139 " pdb=" CA ILE A 139 " pdb=" CG1 ILE A 139 " pdb=" CG2 ILE A 139 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CB VAL A 206 " pdb=" CA VAL A 206 " pdb=" CG1 VAL A 206 " pdb=" CG2 VAL A 206 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.60e-01 chirality pdb=" CA GLU A 455 " pdb=" N GLU A 455 " pdb=" C GLU A 455 " pdb=" CB GLU A 455 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.12e-01 ... (remaining 572 not shown) Planarity restraints: 660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 607 " 0.033 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO A 608 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 608 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 608 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 593 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C ILE A 593 " 0.029 2.00e-02 2.50e+03 pdb=" O ILE A 593 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU A 594 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 9 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.61e+00 pdb=" C VAL A 9 " -0.028 2.00e-02 2.50e+03 pdb=" O VAL A 9 " 0.010 2.00e-02 2.50e+03 pdb=" N CYS A 10 " 0.009 2.00e-02 2.50e+03 ... (remaining 657 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1111 2.83 - 3.35: 3743 3.35 - 3.86: 6350 3.86 - 4.38: 6773 4.38 - 4.90: 11211 Nonbonded interactions: 29188 Sorted by model distance: nonbonded pdb=" OH TYR A 481 " pdb=" OD1 ASN A 510 " model vdw 2.313 2.440 nonbonded pdb=" O GLN A 197 " pdb=" OG SER A 200 " model vdw 2.341 2.440 nonbonded pdb=" O LEU A 606 " pdb=" OG1 THR A 609 " model vdw 2.359 2.440 nonbonded pdb=" O SER A 35 " pdb=" OG SER A 38 " model vdw 2.360 2.440 nonbonded pdb=" O TYR A 317 " pdb=" OG1 THR A 320 " model vdw 2.409 2.440 ... (remaining 29183 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 24 5.16 5 C 2440 2.51 5 N 657 2.21 5 O 687 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 group one per residue 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: 0.220 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: 1.560 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.030 Process input model: 13.390 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.240 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 17.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5474 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 : 0.004 0.059 3881 Z= 0.248 Angle : 0.986 11.151 5222 Z= 0.492 Chirality : 0.052 0.278 575 Planarity : 0.006 0.049 660 Dihedral : 15.638 78.940 1461 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: -3.85 (0.31), residues: 445 helix: -1.84 (0.20), residues: 379 sheet: None (None), residues: 0 loop : -5.66 (0.50), residues: 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 150 average time/residue: 0.2334 time to fit residues: 40.4761 Evaluate side-chains 90 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 0.406 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0375 time to fit residues: 0.7460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 36 optimal weight: 0.0870 chunk 13 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 overall best weight: 1.3760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 HIS A 324 ASN A 330 GLN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5799 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 3881 Z= 0.188 Angle : 0.723 7.185 5222 Z= 0.369 Chirality : 0.039 0.144 575 Planarity : 0.005 0.042 660 Dihedral : 5.220 22.121 505 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: -1.01 (0.38), residues: 445 helix: 0.11 (0.25), residues: 383 sheet: None (None), residues: 0 loop : -5.26 (0.55), residues: 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 110 average time/residue: 0.1958 time to fit residues: 25.4507 Evaluate side-chains 80 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 0.446 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0647 time to fit residues: 0.7248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 41 optimal weight: 0.4980 chunk 45 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 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 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 GLN A 232 HIS A 252 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5771 moved from start: 0.5402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 3881 Z= 0.157 Angle : 0.728 10.728 5222 Z= 0.357 Chirality : 0.040 0.139 575 Planarity : 0.004 0.044 660 Dihedral : 4.982 20.720 505 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.40), residues: 445 helix: 0.78 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -5.29 (0.53), residues: 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 103 average time/residue: 0.1914 time to fit residues: 23.6304 Evaluate side-chains 76 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.452 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 0.0060 chunk 44 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 chunk 11 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 1.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS A 324 ASN A 470 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5952 moved from start: 0.6302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 3881 Z= 0.206 Angle : 0.739 9.287 5222 Z= 0.377 Chirality : 0.042 0.139 575 Planarity : 0.005 0.051 660 Dihedral : 5.068 22.028 505 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 0.11 (0.39), residues: 445 helix: 0.94 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -5.13 (0.56), residues: 65 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 101 average time/residue: 0.1835 time to fit residues: 22.2557 Evaluate side-chains 77 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.457 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5968 moved from start: 0.6654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 3881 Z= 0.173 Angle : 0.730 7.865 5222 Z= 0.365 Chirality : 0.041 0.126 575 Planarity : 0.004 0.045 660 Dihedral : 5.061 20.406 505 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.39), residues: 445 helix: 1.03 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -5.26 (0.49), residues: 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1841 time to fit residues: 23.2956 Evaluate side-chains 79 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.455 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 26 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 36 optimal weight: 0.0170 chunk 20 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5952 moved from start: 0.6927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 3881 Z= 0.159 Angle : 0.723 8.612 5222 Z= 0.355 Chirality : 0.042 0.156 575 Planarity : 0.004 0.047 660 Dihedral : 4.948 19.575 505 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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 (0.39), residues: 445 helix: 1.13 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -5.21 (0.51), residues: 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1829 time to fit residues: 22.5230 Evaluate side-chains 81 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.452 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 44 optimal weight: 0.0070 chunk 27 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 13 optimal weight: 0.0670 chunk 8 optimal weight: 4.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5955 moved from start: 0.7194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 3881 Z= 0.179 Angle : 0.768 7.716 5222 Z= 0.386 Chirality : 0.045 0.291 575 Planarity : 0.004 0.047 660 Dihedral : 5.046 19.274 505 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 0.26 (0.39), residues: 445 helix: 1.02 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -5.12 (0.52), residues: 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1955 time to fit residues: 22.0613 Evaluate side-chains 75 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.455 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 HIS ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5997 moved from start: 0.7665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 3881 Z= 0.191 Angle : 0.771 7.797 5222 Z= 0.390 Chirality : 0.043 0.178 575 Planarity : 0.004 0.045 660 Dihedral : 5.019 20.507 505 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 0.35 (0.40), residues: 445 helix: 1.04 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -4.79 (0.56), residues: 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1956 time to fit residues: 21.4814 Evaluate side-chains 78 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.458 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6083 moved from start: 0.8233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 3881 Z= 0.207 Angle : 0.803 7.541 5222 Z= 0.409 Chirality : 0.045 0.150 575 Planarity : 0.005 0.046 660 Dihedral : 5.152 20.840 505 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 0.11 (0.39), residues: 445 helix: 0.85 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -4.57 (0.58), residues: 64 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.2091 time to fit residues: 24.1459 Evaluate side-chains 78 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.478 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 45 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6029 moved from start: 0.8532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 3881 Z= 0.192 Angle : 0.807 7.470 5222 Z= 0.416 Chirality : 0.047 0.250 575 Planarity : 0.005 0.047 660 Dihedral : 5.089 19.495 505 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 0.14 (0.39), residues: 445 helix: 0.85 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -4.62 (0.59), residues: 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1939 time to fit residues: 22.6509 Evaluate side-chains 79 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.449 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 36 optimal weight: 0.0170 chunk 15 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 2 optimal weight: 0.0570 chunk 26 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 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 = 0.4229 r_free = 0.4229 target = 0.142939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.114563 restraints weight = 16055.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.117311 restraints weight = 12609.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.119659 restraints weight = 10480.259| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6024 moved from start: 0.8790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 3881 Z= 0.215 Angle : 0.813 7.903 5222 Z= 0.423 Chirality : 0.045 0.210 575 Planarity : 0.005 0.047 660 Dihedral : 5.067 20.643 505 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 21.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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 (0.39), residues: 445 helix: 0.75 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -4.61 (0.57), residues: 63 =============================================================================== Job complete usr+sys time: 1139.20 seconds wall clock time: 21 minutes 22.22 seconds (1282.22 seconds total)