Starting phenix.real_space_refine on Sun Mar 10 18:03:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zpg_11338/03_2024/6zpg_11338.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zpg_11338/03_2024/6zpg_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_11338/03_2024/6zpg_11338.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zpg_11338/03_2024/6zpg_11338.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zpg_11338/03_2024/6zpg_11338.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zpg_11338/03_2024/6zpg_11338.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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. Process input model Symmetric amino acids flipped Residue "A GLU 23": "OE1" <-> "OE2" Residue "A TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 115": "OE1" <-> "OE2" Residue "A GLU 151": "OE1" <-> "OE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 163": "OE1" <-> "OE2" Residue "A TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 425": "OD1" <-> "OD2" Residue "A GLU 437": "OE1" <-> "OE2" Residue "A ASP 460": "OD1" <-> "OD2" Residue "A TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 486": "OD1" <-> "OD2" Residue "A ASP 561": "OD1" <-> "OD2" Residue "A GLU 574": "OE1" <-> "OE2" Residue "A GLU 592": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 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: {'CIS': 1, 'PTRANS': 12, 'TRANS': 449} Chain breaks: 8 Time building chain proxies: 2.54, per 1000 atoms: 0.67 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 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 843.1 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: 0.37 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: 0.99 Time building geometry restraints manager: 1.50 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 GLY A 414 " pdb=" N TYR A 415 " pdb=" CA TYR A 415 " ideal model delta sigma weight residual 121.70 128.25 -6.55 1.80e+00 3.09e-01 1.32e+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 ... (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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.470 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.050 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5636 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 : 0.987 11.151 5222 Z= 0.494 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 % Allowed : 6.88 % Favored : 92.87 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 314 HIS 0.013 0.001 HIS A 447 PHE 0.011 0.001 PHE A 409 TYR 0.015 0.001 TYR A 576 ARG 0.001 0.000 ARG A 127 *********************** 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 : 0.401 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: A 13 PHE cc_start: 0.6118 (m-10) cc_final: 0.5915 (m-10) REVERT: A 37 TYR cc_start: 0.7503 (t80) cc_final: 0.6809 (t80) REVERT: A 154 GLU cc_start: 0.8716 (tp30) cc_final: 0.8202 (mm-30) REVERT: A 166 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8794 (mm-30) REVERT: A 223 MET cc_start: 0.7213 (mmm) cc_final: 0.6816 (mmm) REVERT: A 312 ARG cc_start: 0.8687 (mmt180) cc_final: 0.8375 (mmm160) REVERT: A 322 MET cc_start: 0.8861 (mmt) cc_final: 0.8541 (tpp) REVERT: A 448 LYS cc_start: 0.8720 (tptt) cc_final: 0.8203 (tmtt) REVERT: A 481 TYR cc_start: 0.6252 (t80) cc_final: 0.4500 (m-80) REVERT: A 484 MET cc_start: 0.9002 (mtm) cc_final: 0.8654 (mtp) REVERT: A 580 VAL cc_start: 0.7151 (p) cc_final: 0.6706 (t) outliers start: 1 outliers final: 1 residues processed: 150 average time/residue: 0.2364 time to fit residues: 40.5665 Evaluate side-chains 95 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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: 1.9990 chunk 34 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 36 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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: 0.5912 moved from start: 0.4223 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= 0.177 Angle : 0.730 9.034 5222 Z= 0.367 Chirality : 0.039 0.139 575 Planarity : 0.005 0.043 660 Dihedral : 5.250 22.131 505 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.25 % Allowed : 3.93 % Favored : 95.82 % 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: -1.26 (0.37), residues: 445 helix: -0.05 (0.24), residues: 383 sheet: None (None), residues: 0 loop : -5.35 (0.56), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 314 HIS 0.011 0.001 HIS A 447 PHE 0.008 0.001 PHE A 409 TYR 0.021 0.002 TYR A 516 ARG 0.006 0.001 ARG A 496 *********************** 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 113 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 0.460 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 revert: symmetry clash REVERT: A 1 MET cc_start: 0.2409 (ttt) cc_final: 0.1316 (tmm) REVERT: A 110 GLU cc_start: 0.8440 (tp30) cc_final: 0.8117 (tp30) REVERT: A 149 TRP cc_start: 0.7357 (m100) cc_final: 0.6958 (m100) REVERT: A 154 GLU cc_start: 0.8574 (tp30) cc_final: 0.8327 (tm-30) REVERT: A 166 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8813 (mm-30) REVERT: A 256 LEU cc_start: 0.9285 (mm) cc_final: 0.8754 (mm) REVERT: A 260 TYR cc_start: 0.9426 (m-10) cc_final: 0.9033 (m-10) REVERT: A 398 LEU cc_start: 0.7310 (tt) cc_final: 0.6984 (tt) REVERT: A 440 MET cc_start: 0.9026 (mmt) cc_final: 0.8608 (mmm) REVERT: A 448 LYS cc_start: 0.8823 (tptt) cc_final: 0.8194 (tmtt) REVERT: A 573 LEU cc_start: 0.7409 (mm) cc_final: 0.7077 (mm) REVERT: A 580 VAL cc_start: 0.7203 (p) cc_final: 0.6787 (t) REVERT: A 601 LYS cc_start: 0.9515 (ttmt) cc_final: 0.9010 (mtpt) outliers start: 1 outliers final: 1 residues processed: 113 average time/residue: 0.2043 time to fit residues: 27.2443 Evaluate side-chains 83 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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: 3.9990 chunk 12 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 159 GLN A 232 HIS ** A 474 GLN ** 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: 0.5090 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= 0.168 Angle : 0.721 10.298 5222 Z= 0.362 Chirality : 0.040 0.141 575 Planarity : 0.004 0.048 660 Dihedral : 5.006 21.361 505 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % 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: -0.08 (0.40), residues: 445 helix: 0.78 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -5.04 (0.63), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 314 HIS 0.011 0.001 HIS A 447 PHE 0.019 0.002 PHE A 410 TYR 0.021 0.002 TYR A 576 ARG 0.004 0.001 ARG A 496 *********************** 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 105 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.429 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: A 1 MET cc_start: 0.2787 (ttt) cc_final: 0.1630 (tmm) REVERT: A 37 TYR cc_start: 0.7644 (t80) cc_final: 0.7067 (t80) REVERT: A 110 GLU cc_start: 0.8240 (tp30) cc_final: 0.8026 (tp30) REVERT: A 149 TRP cc_start: 0.7394 (m100) cc_final: 0.7008 (m100) REVERT: A 154 GLU cc_start: 0.8576 (tp30) cc_final: 0.8251 (mm-30) REVERT: A 166 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8893 (mm-30) REVERT: A 256 LEU cc_start: 0.9262 (mm) cc_final: 0.8834 (mm) REVERT: A 258 GLN cc_start: 0.9260 (mm-40) cc_final: 0.8573 (mm-40) REVERT: A 260 TYR cc_start: 0.9424 (m-10) cc_final: 0.9069 (m-10) REVERT: A 266 PHE cc_start: 0.5027 (p90) cc_final: 0.4822 (p90) REVERT: A 267 MET cc_start: 0.7089 (mmm) cc_final: 0.6624 (mmm) REVERT: A 312 ARG cc_start: 0.8469 (mmm160) cc_final: 0.7977 (ptp-170) REVERT: A 316 LYS cc_start: 0.8996 (ptpp) cc_final: 0.8232 (pttm) REVERT: A 322 MET cc_start: 0.9216 (tpt) cc_final: 0.8992 (tmm) REVERT: A 398 LEU cc_start: 0.7733 (tt) cc_final: 0.7417 (mm) REVERT: A 448 LYS cc_start: 0.8879 (tptt) cc_final: 0.8393 (tmtt) REVERT: A 475 PHE cc_start: 0.8786 (t80) cc_final: 0.8332 (t80) REVERT: A 481 TYR cc_start: 0.6363 (t80) cc_final: 0.5014 (m-80) REVERT: A 544 MET cc_start: 0.6519 (ptm) cc_final: 0.6147 (ptm) REVERT: A 580 VAL cc_start: 0.7673 (p) cc_final: 0.7259 (t) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2078 time to fit residues: 25.6793 Evaluate side-chains 84 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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: 5.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 41 optimal weight: 0.0870 chunk 44 optimal weight: 0.0370 chunk 39 optimal weight: 0.0010 chunk 11 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.6244 ------------------------------------------------------------------------------- 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 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 ASN A 470 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: 0.5976 moved from start: 0.5468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3881 Z= 0.155 Angle : 0.697 9.457 5222 Z= 0.351 Chirality : 0.040 0.129 575 Planarity : 0.004 0.050 660 Dihedral : 4.931 20.072 505 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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: 0.22 (0.40), residues: 445 helix: 0.98 (0.26), residues: 384 sheet: None (None), residues: 0 loop : -5.23 (0.55), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 149 HIS 0.011 0.001 HIS A 447 PHE 0.018 0.001 PHE A 410 TYR 0.022 0.002 TYR A 516 ARG 0.003 0.000 ARG A 306 *********************** 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 105 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.461 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 revert: symmetry clash REVERT: A 37 TYR cc_start: 0.7592 (t80) cc_final: 0.7029 (t80) REVERT: A 110 GLU cc_start: 0.8270 (tp30) cc_final: 0.8053 (tp30) REVERT: A 149 TRP cc_start: 0.7315 (m100) cc_final: 0.6884 (m100) REVERT: A 154 GLU cc_start: 0.8538 (tp30) cc_final: 0.8245 (mm-30) REVERT: A 166 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8863 (mm-30) REVERT: A 209 HIS cc_start: 0.8606 (m90) cc_final: 0.8327 (m-70) REVERT: A 258 GLN cc_start: 0.9323 (mm-40) cc_final: 0.8710 (mm-40) REVERT: A 266 PHE cc_start: 0.4758 (p90) cc_final: 0.4519 (p90) REVERT: A 267 MET cc_start: 0.7329 (mmm) cc_final: 0.6920 (mmm) REVERT: A 312 ARG cc_start: 0.8487 (mmm160) cc_final: 0.7962 (ptp-170) REVERT: A 316 LYS cc_start: 0.8968 (ptpp) cc_final: 0.8231 (pttm) REVERT: A 322 MET cc_start: 0.9216 (tpt) cc_final: 0.8989 (tmm) REVERT: A 398 LEU cc_start: 0.7393 (tt) cc_final: 0.7161 (mm) REVERT: A 448 LYS cc_start: 0.8877 (tptt) cc_final: 0.8210 (tmtt) REVERT: A 475 PHE cc_start: 0.8765 (t80) cc_final: 0.8350 (t80) REVERT: A 544 MET cc_start: 0.6335 (ptm) cc_final: 0.6081 (ptm) REVERT: A 580 VAL cc_start: 0.7952 (p) cc_final: 0.7540 (t) REVERT: A 601 LYS cc_start: 0.9512 (ttmt) cc_final: 0.9231 (mmtt) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2058 time to fit residues: 25.4571 Evaluate side-chains 84 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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: 4.9990 chunk 18 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN A 324 ASN A 470 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6151 moved from start: 0.6460 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= 0.177 Angle : 0.718 7.768 5222 Z= 0.362 Chirality : 0.041 0.142 575 Planarity : 0.005 0.045 660 Dihedral : 4.945 21.371 505 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.25 % Allowed : 3.93 % Favored : 95.82 % 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: 0.39 (0.39), residues: 445 helix: 1.09 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -4.80 (0.58), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 314 HIS 0.010 0.001 HIS A 447 PHE 0.016 0.002 PHE A 409 TYR 0.023 0.002 TYR A 582 ARG 0.004 0.000 ARG A 393 *********************** 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 107 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 0.439 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 REVERT: A 37 TYR cc_start: 0.7684 (t80) cc_final: 0.7176 (t80) REVERT: A 110 GLU cc_start: 0.8479 (tp30) cc_final: 0.8233 (tp30) REVERT: A 115 GLU cc_start: 0.8515 (pt0) cc_final: 0.8282 (pt0) REVERT: A 126 ARG cc_start: 0.7780 (ptt90) cc_final: 0.7501 (ptt90) REVERT: A 154 GLU cc_start: 0.8616 (tp30) cc_final: 0.8244 (mm-30) REVERT: A 209 HIS cc_start: 0.8547 (m90) cc_final: 0.8242 (m-70) REVERT: A 252 ASN cc_start: 0.9273 (m-40) cc_final: 0.9045 (m-40) REVERT: A 258 GLN cc_start: 0.9291 (mm110) cc_final: 0.8655 (mm-40) REVERT: A 312 ARG cc_start: 0.8684 (mmm160) cc_final: 0.8102 (ptp-170) REVERT: A 316 LYS cc_start: 0.9044 (ptpp) cc_final: 0.8469 (ptpt) REVERT: A 322 MET cc_start: 0.9229 (tpt) cc_final: 0.9007 (tmm) REVERT: A 398 LEU cc_start: 0.7588 (tt) cc_final: 0.6972 (tt) REVERT: A 448 LYS cc_start: 0.8920 (tptt) cc_final: 0.8540 (tmtt) REVERT: A 470 ASN cc_start: 0.8750 (m-40) cc_final: 0.8418 (m-40) REVERT: A 544 MET cc_start: 0.6451 (ptm) cc_final: 0.6111 (ptm) REVERT: A 601 LYS cc_start: 0.9582 (ttmt) cc_final: 0.9327 (mttt) outliers start: 1 outliers final: 1 residues processed: 107 average time/residue: 0.1869 time to fit residues: 23.7372 Evaluate side-chains 89 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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: 1.9990 chunk 10 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 3 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6150 moved from start: 0.6859 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= 0.170 Angle : 0.749 10.285 5222 Z= 0.374 Chirality : 0.043 0.146 575 Planarity : 0.004 0.046 660 Dihedral : 5.006 20.320 505 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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: 1.00 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -4.83 (0.55), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 149 HIS 0.012 0.001 HIS A 447 PHE 0.013 0.001 PHE A 409 TYR 0.024 0.002 TYR A 402 ARG 0.002 0.000 ARG A 393 *********************** 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 103 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.338 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 revert: symmetry clash REVERT: A 37 TYR cc_start: 0.7699 (t80) cc_final: 0.7153 (t80) REVERT: A 110 GLU cc_start: 0.8431 (tp30) cc_final: 0.8216 (tp30) REVERT: A 115 GLU cc_start: 0.8534 (pt0) cc_final: 0.8295 (pt0) REVERT: A 154 GLU cc_start: 0.8622 (tp30) cc_final: 0.8225 (mm-30) REVERT: A 209 HIS cc_start: 0.8500 (m90) cc_final: 0.8270 (m-70) REVERT: A 252 ASN cc_start: 0.9248 (m-40) cc_final: 0.9036 (m-40) REVERT: A 258 GLN cc_start: 0.9297 (mm110) cc_final: 0.8654 (mm-40) REVERT: A 260 TYR cc_start: 0.9415 (m-10) cc_final: 0.9119 (m-10) REVERT: A 312 ARG cc_start: 0.8674 (mmm160) cc_final: 0.8209 (ptp-170) REVERT: A 316 LYS cc_start: 0.9041 (ptpp) cc_final: 0.8239 (ptpp) REVERT: A 322 MET cc_start: 0.9217 (tpt) cc_final: 0.9006 (tmm) REVERT: A 437 GLU cc_start: 0.8524 (pm20) cc_final: 0.8210 (pt0) REVERT: A 448 LYS cc_start: 0.9094 (tptt) cc_final: 0.8553 (tmtt) REVERT: A 470 ASN cc_start: 0.8741 (m110) cc_final: 0.8494 (m110) REVERT: A 544 MET cc_start: 0.6511 (ptm) cc_final: 0.6203 (ptm) REVERT: A 601 LYS cc_start: 0.9588 (ttmt) cc_final: 0.9334 (mttt) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.2041 time to fit residues: 24.8539 Evaluate side-chains 87 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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: 4.9990 chunk 25 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 252 ASN A 470 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6204 moved from start: 0.7264 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= 0.191 Angle : 0.754 8.243 5222 Z= 0.379 Chirality : 0.044 0.183 575 Planarity : 0.005 0.074 660 Dihedral : 5.013 20.590 505 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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: 0.31 (0.39), residues: 445 helix: 0.98 (0.25), residues: 383 sheet: None (None), residues: 0 loop : -4.71 (0.58), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 149 HIS 0.012 0.002 HIS A 447 PHE 0.015 0.001 PHE A 409 TYR 0.022 0.002 TYR A 576 ARG 0.006 0.000 ARG A 127 *********************** 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 105 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.415 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 REVERT: A 110 GLU cc_start: 0.8586 (tp30) cc_final: 0.8369 (tp30) REVERT: A 144 ASN cc_start: 0.9182 (m-40) cc_final: 0.8968 (m-40) REVERT: A 154 GLU cc_start: 0.8672 (tp30) cc_final: 0.8249 (mm-30) REVERT: A 209 HIS cc_start: 0.8578 (m90) cc_final: 0.8276 (m-70) REVERT: A 252 ASN cc_start: 0.9244 (m110) cc_final: 0.9011 (m-40) REVERT: A 258 GLN cc_start: 0.9311 (mm110) cc_final: 0.8638 (mm-40) REVERT: A 271 HIS cc_start: 0.7074 (t-90) cc_final: 0.6475 (m170) REVERT: A 277 ASN cc_start: 0.8838 (m110) cc_final: 0.8564 (m110) REVERT: A 312 ARG cc_start: 0.8701 (mmm160) cc_final: 0.8140 (ptp-170) REVERT: A 316 LYS cc_start: 0.9074 (ptpp) cc_final: 0.8203 (ptpp) REVERT: A 322 MET cc_start: 0.9230 (tpt) cc_final: 0.9020 (tmm) REVERT: A 437 GLU cc_start: 0.8566 (pm20) cc_final: 0.8225 (pt0) REVERT: A 448 LYS cc_start: 0.9115 (tptt) cc_final: 0.8594 (tmtt) REVERT: A 470 ASN cc_start: 0.8761 (m-40) cc_final: 0.8474 (m-40) REVERT: A 544 MET cc_start: 0.6349 (ptm) cc_final: 0.6088 (ptm) REVERT: A 547 LYS cc_start: 0.8283 (tttm) cc_final: 0.8019 (mtpt) REVERT: A 601 LYS cc_start: 0.9595 (ttmt) cc_final: 0.9339 (mttt) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1909 time to fit residues: 23.8445 Evaluate side-chains 88 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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: 0.9980 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 41 optimal weight: 0.0570 chunk 24 optimal weight: 0.9980 overall best weight: 0.7498 ------------------------------------------------------------------------------- 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 324 ASN A 470 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 moved from start: 0.7386 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= 0.170 Angle : 0.757 7.750 5222 Z= 0.379 Chirality : 0.044 0.181 575 Planarity : 0.004 0.046 660 Dihedral : 4.974 19.174 505 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % 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: 0.48 (0.39), residues: 445 helix: 1.06 (0.25), residues: 385 sheet: None (None), residues: 0 loop : -4.55 (0.61), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 149 HIS 0.013 0.001 HIS A 447 PHE 0.018 0.001 PHE A 13 TYR 0.023 0.001 TYR A 576 ARG 0.003 0.000 ARG A 93 *********************** 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 102 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.434 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: A 37 TYR cc_start: 0.7681 (t80) cc_final: 0.7083 (t80) REVERT: A 110 GLU cc_start: 0.8428 (tp30) cc_final: 0.8228 (tp30) REVERT: A 144 ASN cc_start: 0.9186 (m-40) cc_final: 0.8923 (m-40) REVERT: A 154 GLU cc_start: 0.8672 (tp30) cc_final: 0.8258 (mm-30) REVERT: A 209 HIS cc_start: 0.8546 (m90) cc_final: 0.8264 (m-70) REVERT: A 258 GLN cc_start: 0.9323 (mm110) cc_final: 0.8677 (mm-40) REVERT: A 267 MET cc_start: 0.7461 (mmm) cc_final: 0.6772 (mmm) REVERT: A 271 HIS cc_start: 0.7012 (t-90) cc_final: 0.6418 (m170) REVERT: A 277 ASN cc_start: 0.8814 (m110) cc_final: 0.8538 (m110) REVERT: A 312 ARG cc_start: 0.8681 (mmm160) cc_final: 0.8132 (ptp-170) REVERT: A 398 LEU cc_start: 0.8439 (pp) cc_final: 0.7987 (tp) REVERT: A 437 GLU cc_start: 0.8553 (pm20) cc_final: 0.8186 (pt0) REVERT: A 448 LYS cc_start: 0.9085 (tptt) cc_final: 0.8595 (tmtt) REVERT: A 470 ASN cc_start: 0.8843 (m110) cc_final: 0.8555 (m110) REVERT: A 544 MET cc_start: 0.6286 (ptm) cc_final: 0.6031 (ptm) REVERT: A 547 LYS cc_start: 0.8214 (tttm) cc_final: 0.7954 (mtpt) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1939 time to fit residues: 23.5601 Evaluate side-chains 88 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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: 5.9990 chunk 32 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 HIS ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 ASN A 470 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: 0.6333 moved from start: 0.8089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3881 Z= 0.224 Angle : 0.810 8.805 5222 Z= 0.415 Chirality : 0.046 0.176 575 Planarity : 0.005 0.045 660 Dihedral : 5.272 23.810 505 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 22.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % 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: 0.12 (0.39), residues: 445 helix: 0.80 (0.25), residues: 383 sheet: None (None), residues: 0 loop : -4.32 (0.65), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP A 149 HIS 0.012 0.002 HIS A 447 PHE 0.018 0.002 PHE A 13 TYR 0.031 0.002 TYR A 576 ARG 0.004 0.001 ARG A 393 *********************** 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 108 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.455 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: A 12 LYS cc_start: 0.8632 (mmpt) cc_final: 0.8399 (mmmt) REVERT: A 144 ASN cc_start: 0.9225 (m-40) cc_final: 0.8990 (m-40) REVERT: A 154 GLU cc_start: 0.8731 (tp30) cc_final: 0.8141 (mm-30) REVERT: A 209 HIS cc_start: 0.8530 (m90) cc_final: 0.8290 (m-70) REVERT: A 252 ASN cc_start: 0.9317 (m-40) cc_final: 0.9097 (m-40) REVERT: A 258 GLN cc_start: 0.9362 (mm110) cc_final: 0.8678 (mm-40) REVERT: A 271 HIS cc_start: 0.6787 (t-90) cc_final: 0.6181 (m170) REVERT: A 277 ASN cc_start: 0.8896 (m110) cc_final: 0.8609 (m110) REVERT: A 312 ARG cc_start: 0.8756 (mmm160) cc_final: 0.7990 (ptp-170) REVERT: A 316 LYS cc_start: 0.9103 (ptpp) cc_final: 0.8298 (ptpp) REVERT: A 437 GLU cc_start: 0.8663 (pm20) cc_final: 0.8298 (pt0) REVERT: A 448 LYS cc_start: 0.9173 (tptt) cc_final: 0.8717 (tmtt) REVERT: A 470 ASN cc_start: 0.8667 (m-40) cc_final: 0.8301 (m-40) REVERT: A 547 LYS cc_start: 0.8240 (tttm) cc_final: 0.7967 (mtpt) REVERT: A 573 LEU cc_start: 0.7555 (mm) cc_final: 0.7147 (mm) REVERT: A 601 LYS cc_start: 0.9608 (ttmt) cc_final: 0.9273 (mmtt) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1814 time to fit residues: 23.3909 Evaluate side-chains 92 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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: 7.9990 chunk 42 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 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: 0.6311 moved from start: 0.8355 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= 0.187 Angle : 0.768 8.017 5222 Z= 0.386 Chirality : 0.044 0.167 575 Planarity : 0.004 0.046 660 Dihedral : 5.092 19.287 505 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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: 0.29 (0.39), residues: 445 helix: 0.89 (0.25), residues: 385 sheet: None (None), residues: 0 loop : -4.27 (0.67), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 149 HIS 0.014 0.001 HIS A 447 PHE 0.015 0.001 PHE A 475 TYR 0.026 0.002 TYR A 576 ARG 0.003 0.000 ARG A 549 ********************** 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 111 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.446 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: A 12 LYS cc_start: 0.8497 (mmpt) cc_final: 0.8241 (mmmt) REVERT: A 144 ASN cc_start: 0.9237 (m-40) cc_final: 0.9000 (m-40) REVERT: A 149 TRP cc_start: 0.7485 (m100) cc_final: 0.7206 (m100) REVERT: A 154 GLU cc_start: 0.8740 (tp30) cc_final: 0.8210 (mm-30) REVERT: A 209 HIS cc_start: 0.8561 (m90) cc_final: 0.8353 (m-70) REVERT: A 258 GLN cc_start: 0.9374 (mm110) cc_final: 0.8664 (mm-40) REVERT: A 267 MET cc_start: 0.7342 (mmm) cc_final: 0.6607 (mmm) REVERT: A 271 HIS cc_start: 0.7063 (t-90) cc_final: 0.6435 (m170) REVERT: A 277 ASN cc_start: 0.8913 (m110) cc_final: 0.8633 (m110) REVERT: A 312 ARG cc_start: 0.8751 (mmm160) cc_final: 0.8034 (ptp-170) REVERT: A 316 LYS cc_start: 0.9097 (ptpp) cc_final: 0.8296 (ptpp) REVERT: A 329 MET cc_start: 0.2330 (tpp) cc_final: 0.2080 (tpp) REVERT: A 398 LEU cc_start: 0.8682 (pp) cc_final: 0.8213 (tp) REVERT: A 437 GLU cc_start: 0.8522 (pm20) cc_final: 0.8191 (pt0) REVERT: A 448 LYS cc_start: 0.9150 (tptt) cc_final: 0.8751 (tmtt) REVERT: A 470 ASN cc_start: 0.8652 (m110) cc_final: 0.8351 (m110) REVERT: A 544 MET cc_start: 0.6402 (ptm) cc_final: 0.6062 (ptt) REVERT: A 547 LYS cc_start: 0.8249 (tttm) cc_final: 0.8009 (mtpt) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1837 time to fit residues: 24.3910 Evaluate side-chains 95 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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: 7.9990 chunk 15 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 2 optimal weight: 0.0770 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 ASN A 470 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.143828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.120225 restraints weight = 19087.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.122674 restraints weight = 15461.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.124699 restraints weight = 12994.817| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6436 moved from start: 0.8517 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= 0.199 Angle : 0.824 8.790 5222 Z= 0.417 Chirality : 0.045 0.153 575 Planarity : 0.004 0.047 660 Dihedral : 5.078 19.325 505 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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: 0.30 (0.39), residues: 445 helix: 0.90 (0.25), residues: 384 sheet: None (None), residues: 0 loop : -4.20 (0.67), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 149 HIS 0.012 0.001 HIS A 447 PHE 0.012 0.001 PHE A 409 TYR 0.024 0.002 TYR A 576 ARG 0.003 0.000 ARG A 123 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1174.64 seconds wall clock time: 21 minutes 53.85 seconds (1313.85 seconds total)