Starting phenix.real_space_refine on Wed Mar 5 21:53:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zpg_11338/03_2025/6zpg_11338.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zpg_11338/03_2025/6zpg_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/cci-nas-00/data/ceres_data/6zpg_11338/03_2025/6zpg_11338.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zpg_11338/03_2025/6zpg_11338.map" model { file = "/net/cci-nas-00/data/ceres_data/6zpg_11338/03_2025/6zpg_11338.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zpg_11338/03_2025/6zpg_11338.cif" } 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. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 2.75, per 1000 atoms: 0.72 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 - 3.00 Amino acid : True - 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: 1.12 Conformation dependent library (CDL) restraints added in 446.2 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: 0.31 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: 0.97 Time building geometry restraints manager: 1.13 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: 0.00 - 2.23: 5052 2.23 - 4.46: 129 4.46 - 6.69: 21 6.69 - 8.92: 12 8.92 - 11.15: 8 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 3.040 nonbonded pdb=" O GLN A 197 " pdb=" OG SER A 200 " model vdw 2.341 3.040 nonbonded pdb=" O LEU A 606 " pdb=" OG1 THR A 609 " model vdw 2.359 3.040 nonbonded pdb=" O SER A 35 " pdb=" OG SER A 38 " model vdw 2.360 3.040 nonbonded pdb=" O TYR A 317 " pdb=" OG1 THR A 320 " model vdw 2.409 3.040 ... (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: 0.540 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.740 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.570 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 0.441 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: 0.2436 time to fit residues: 41.8481 Evaluate side-chains 95 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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: 3.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 GLN A 271 HIS A 479 HIS A 501 HIS A 568 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.158432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.129882 restraints weight = 15392.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.133078 restraints weight = 11815.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.135641 restraints weight = 9617.597| |-----------------------------------------------------------------------------| r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6115 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3881 Z= 0.174 Angle : 0.733 9.248 5222 Z= 0.370 Chirality : 0.040 0.141 575 Planarity : 0.005 0.043 660 Dihedral : 5.283 22.916 505 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.25 % Allowed : 4.42 % Favored : 95.33 % 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: -1.46 (0.36), residues: 445 helix: -0.19 (0.24), residues: 383 sheet: None (None), residues: 0 loop : -5.45 (0.53), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 314 HIS 0.011 0.001 HIS A 447 PHE 0.007 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 116 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.452 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 1 MET cc_start: 0.1835 (ttt) cc_final: 0.0990 (tmm) REVERT: A 110 GLU cc_start: 0.9105 (tp30) cc_final: 0.8853 (tp30) REVERT: A 111 LEU cc_start: 0.7653 (mp) cc_final: 0.7362 (pp) REVERT: A 115 GLU cc_start: 0.8694 (pt0) cc_final: 0.8443 (pt0) REVERT: A 149 TRP cc_start: 0.7869 (m100) cc_final: 0.7411 (m100) REVERT: A 154 GLU cc_start: 0.8667 (tp30) cc_final: 0.8363 (tm-30) REVERT: A 159 GLN cc_start: 0.8988 (pp30) cc_final: 0.8755 (tm-30) REVERT: A 166 GLU cc_start: 0.9567 (mm-30) cc_final: 0.9210 (mm-30) REVERT: A 210 ASN cc_start: 0.9594 (t0) cc_final: 0.9365 (p0) REVERT: A 252 ASN cc_start: 0.9364 (t0) cc_final: 0.9157 (t0) REVERT: A 256 LEU cc_start: 0.9489 (mm) cc_final: 0.8968 (mm) REVERT: A 258 GLN cc_start: 0.9279 (tp40) cc_final: 0.9054 (mm-40) REVERT: A 312 ARG cc_start: 0.8804 (mmt180) cc_final: 0.8501 (mmm160) REVERT: A 440 MET cc_start: 0.9085 (mmt) cc_final: 0.8648 (mmm) REVERT: A 447 HIS cc_start: 0.8786 (p90) cc_final: 0.8435 (p90) REVERT: A 448 LYS cc_start: 0.9051 (tptt) cc_final: 0.8405 (tmtt) REVERT: A 484 MET cc_start: 0.9438 (mtm) cc_final: 0.9119 (mtp) REVERT: A 485 MET cc_start: 0.8551 (mmp) cc_final: 0.8122 (mmp) REVERT: A 573 LEU cc_start: 0.7741 (mm) cc_final: 0.7541 (mm) REVERT: A 580 VAL cc_start: 0.7436 (p) cc_final: 0.6961 (t) REVERT: A 601 LYS cc_start: 0.9459 (ttmt) cc_final: 0.9120 (mtpt) outliers start: 1 outliers final: 0 residues processed: 115 average time/residue: 0.2133 time to fit residues: 28.7820 Evaluate side-chains 92 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 31 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 0.1980 chunk 21 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 HIS A 568 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.159797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.131416 restraints weight = 14945.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.134125 restraints weight = 11992.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.136253 restraints weight = 10024.393| |-----------------------------------------------------------------------------| r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6124 moved from start: 0.4847 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= 0.163 Angle : 0.725 10.800 5222 Z= 0.363 Chirality : 0.041 0.126 575 Planarity : 0.004 0.044 660 Dihedral : 5.007 20.558 505 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % 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: -0.25 (0.39), residues: 445 helix: 0.66 (0.25), residues: 381 sheet: None (None), residues: 0 loop : -5.07 (0.59), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 149 HIS 0.010 0.001 HIS A 447 PHE 0.024 0.002 PHE A 410 TYR 0.022 0.002 TYR A 576 ARG 0.005 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 107 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.495 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 1 MET cc_start: 0.2341 (ttt) cc_final: 0.1392 (tmm) REVERT: A 149 TRP cc_start: 0.8059 (m100) cc_final: 0.7595 (m100) REVERT: A 159 GLN cc_start: 0.9067 (pp30) cc_final: 0.8856 (tm-30) REVERT: A 166 GLU cc_start: 0.9515 (mm-30) cc_final: 0.9120 (mm-30) REVERT: A 210 ASN cc_start: 0.9552 (t0) cc_final: 0.9332 (t0) REVERT: A 258 GLN cc_start: 0.9289 (tp40) cc_final: 0.9018 (mm-40) REVERT: A 312 ARG cc_start: 0.8814 (mmt180) cc_final: 0.8489 (mmm160) REVERT: A 316 LYS cc_start: 0.9046 (ptpp) cc_final: 0.8512 (ptpp) REVERT: A 398 LEU cc_start: 0.7914 (tt) cc_final: 0.7601 (mm) REVERT: A 448 LYS cc_start: 0.9026 (tptt) cc_final: 0.8583 (tmtt) REVERT: A 481 TYR cc_start: 0.6985 (t80) cc_final: 0.4403 (m-80) REVERT: A 484 MET cc_start: 0.9447 (mtm) cc_final: 0.9180 (mtp) REVERT: A 544 MET cc_start: 0.6585 (ptm) cc_final: 0.6357 (ptm) REVERT: A 580 VAL cc_start: 0.7819 (p) cc_final: 0.7367 (t) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.2076 time to fit residues: 26.2132 Evaluate side-chains 86 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 20 optimal weight: 0.7980 chunk 7 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 A 209 HIS A 470 ASN A 474 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5061 r_free = 0.5061 target = 0.237891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.5280 r_free = 0.5280 target = 0.217097 restraints weight = 21418.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.5257 r_free = 0.5257 target = 0.219401 restraints weight = 13606.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.5265 r_free = 0.5265 target = 0.220943 restraints weight = 8831.224| |-----------------------------------------------------------------------------| r_work (final): 0.4307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6038 moved from start: 0.5535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3881 Z= 0.167 Angle : 0.713 9.634 5222 Z= 0.362 Chirality : 0.041 0.149 575 Planarity : 0.004 0.052 660 Dihedral : 4.914 20.602 505 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % 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: 0.28 (0.40), residues: 445 helix: 1.03 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -5.10 (0.56), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 314 HIS 0.006 0.001 HIS A 209 PHE 0.016 0.002 PHE A 409 TYR 0.027 0.002 TYR A 402 ARG 0.005 0.001 ARG A 450 *********************** 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 103 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.459 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 159 GLN cc_start: 0.8768 (pp30) cc_final: 0.8550 (tm-30) REVERT: A 166 GLU cc_start: 0.9466 (mm-30) cc_final: 0.9115 (mm-30) REVERT: A 209 HIS cc_start: 0.9319 (m90) cc_final: 0.8998 (m-70) REVERT: A 210 ASN cc_start: 0.9414 (t0) cc_final: 0.9207 (t0) REVERT: A 252 ASN cc_start: 0.9392 (m-40) cc_final: 0.9182 (m-40) REVERT: A 258 GLN cc_start: 0.9327 (tp40) cc_final: 0.9041 (mm-40) REVERT: A 312 ARG cc_start: 0.8795 (mmt180) cc_final: 0.8396 (mmm160) REVERT: A 316 LYS cc_start: 0.9014 (ptpp) cc_final: 0.8506 (ptpt) REVERT: A 448 LYS cc_start: 0.8895 (tptt) cc_final: 0.8353 (tmtt) REVERT: A 481 TYR cc_start: 0.6851 (t80) cc_final: 0.5437 (t80) REVERT: A 483 ASP cc_start: 0.9542 (t70) cc_final: 0.9339 (t0) REVERT: A 484 MET cc_start: 0.9441 (mtm) cc_final: 0.9204 (mmt) REVERT: A 580 VAL cc_start: 0.7977 (p) cc_final: 0.7541 (t) REVERT: A 601 LYS cc_start: 0.9513 (ttmt) cc_final: 0.9296 (mmtm) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1944 time to fit residues: 23.9151 Evaluate side-chains 85 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 5 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 44 optimal weight: 0.0270 chunk 17 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.155656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.123571 restraints weight = 16094.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.125872 restraints weight = 13664.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.127750 restraints weight = 11970.237| |-----------------------------------------------------------------------------| r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 moved from start: 0.6140 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 : 0.730 7.808 5222 Z= 0.373 Chirality : 0.042 0.128 575 Planarity : 0.005 0.046 660 Dihedral : 4.967 21.889 505 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % 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: 0.50 (0.39), residues: 445 helix: 1.18 (0.25), residues: 382 sheet: None (None), residues: 0 loop : -5.00 (0.55), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 149 HIS 0.004 0.001 HIS A 105 PHE 0.018 0.001 PHE A 409 TYR 0.022 0.002 TYR A 576 ARG 0.003 0.000 ARG A 496 *********************** 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 106 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.414 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: 0.8169 (t80) cc_final: 0.7742 (t80) REVERT: A 159 GLN cc_start: 0.8990 (pp30) cc_final: 0.8775 (tm-30) REVERT: A 163 GLU cc_start: 0.9165 (mt-10) cc_final: 0.8692 (pt0) REVERT: A 209 HIS cc_start: 0.9433 (m90) cc_final: 0.9106 (m-70) REVERT: A 230 TYR cc_start: 0.8886 (m-10) cc_final: 0.8612 (m-80) REVERT: A 252 ASN cc_start: 0.9412 (m-40) cc_final: 0.9191 (m-40) REVERT: A 258 GLN cc_start: 0.9369 (tp40) cc_final: 0.9055 (mm-40) REVERT: A 316 LYS cc_start: 0.9085 (ptpp) cc_final: 0.8578 (pttm) REVERT: A 448 LYS cc_start: 0.9025 (tptt) cc_final: 0.8683 (tmtt) REVERT: A 466 TYR cc_start: 0.7771 (t80) cc_final: 0.7517 (t80) REVERT: A 470 ASN cc_start: 0.8935 (m110) cc_final: 0.8413 (m110) REVERT: A 481 TYR cc_start: 0.7177 (t80) cc_final: 0.5205 (m-80) REVERT: A 484 MET cc_start: 0.9426 (mtm) cc_final: 0.9010 (mtp) REVERT: A 509 LEU cc_start: 0.7087 (mt) cc_final: 0.6579 (tt) REVERT: A 601 LYS cc_start: 0.9520 (ttmt) cc_final: 0.9278 (mttp) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1930 time to fit residues: 24.3041 Evaluate side-chains 87 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 27 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.153854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.124089 restraints weight = 14751.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.126438 restraints weight = 12460.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.128320 restraints weight = 10810.680| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 moved from start: 0.6399 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= 0.167 Angle : 0.739 8.556 5222 Z= 0.369 Chirality : 0.042 0.156 575 Planarity : 0.004 0.048 660 Dihedral : 4.881 20.398 505 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % 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: 0.48 (0.39), residues: 445 helix: 1.18 (0.25), residues: 382 sheet: None (None), residues: 0 loop : -5.12 (0.51), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 149 HIS 0.003 0.001 HIS A 447 PHE 0.014 0.001 PHE A 409 TYR 0.022 0.002 TYR A 516 ARG 0.002 0.000 ARG A 450 *********************** 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 106 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.445 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: 0.8198 (t80) cc_final: 0.7695 (t80) REVERT: A 140 GLN cc_start: 0.8446 (mp10) cc_final: 0.8142 (mm-40) REVERT: A 144 ASN cc_start: 0.9469 (m-40) cc_final: 0.9128 (m-40) REVERT: A 149 TRP cc_start: 0.8147 (m100) cc_final: 0.7918 (m100) REVERT: A 159 GLN cc_start: 0.8890 (pp30) cc_final: 0.8659 (tm-30) REVERT: A 163 GLU cc_start: 0.9190 (mt-10) cc_final: 0.8628 (pt0) REVERT: A 209 HIS cc_start: 0.9396 (m90) cc_final: 0.9080 (m-70) REVERT: A 252 ASN cc_start: 0.9379 (m-40) cc_final: 0.9159 (m-40) REVERT: A 258 GLN cc_start: 0.9375 (tp40) cc_final: 0.9067 (mm-40) REVERT: A 312 ARG cc_start: 0.8923 (mmt180) cc_final: 0.8508 (mmm160) REVERT: A 316 LYS cc_start: 0.9034 (ptpp) cc_final: 0.8594 (ptpt) REVERT: A 398 LEU cc_start: 0.8304 (tt) cc_final: 0.8008 (mm) REVERT: A 448 LYS cc_start: 0.9040 (tptt) cc_final: 0.8449 (tmtt) REVERT: A 470 ASN cc_start: 0.8961 (m-40) cc_final: 0.8671 (m-40) REVERT: A 475 PHE cc_start: 0.9287 (t80) cc_final: 0.8986 (t80) REVERT: A 481 TYR cc_start: 0.7049 (t80) cc_final: 0.5951 (t80) REVERT: A 484 MET cc_start: 0.9450 (mtm) cc_final: 0.9248 (mmt) REVERT: A 601 LYS cc_start: 0.9536 (ttmt) cc_final: 0.9285 (mttp) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.2074 time to fit residues: 26.0469 Evaluate side-chains 84 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.153820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.124125 restraints weight = 14024.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.126689 restraints weight = 11632.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.128683 restraints weight = 9972.857| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 moved from start: 0.6800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3881 Z= 0.170 Angle : 0.737 7.435 5222 Z= 0.373 Chirality : 0.042 0.138 575 Planarity : 0.004 0.048 660 Dihedral : 4.868 20.315 505 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % 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: 0.59 (0.39), residues: 445 helix: 1.23 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -4.97 (0.53), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 149 HIS 0.006 0.001 HIS A 117 PHE 0.019 0.001 PHE A 13 TYR 0.021 0.002 TYR A 576 ARG 0.002 0.000 ARG A 450 *********************** 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 102 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 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 revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8207 (t80) cc_final: 0.7678 (t80) REVERT: A 140 GLN cc_start: 0.8432 (mp10) cc_final: 0.8161 (mm-40) REVERT: A 144 ASN cc_start: 0.9439 (m-40) cc_final: 0.9089 (m-40) REVERT: A 159 GLN cc_start: 0.8949 (pp30) cc_final: 0.8728 (tm-30) REVERT: A 163 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8669 (pt0) REVERT: A 209 HIS cc_start: 0.9415 (m90) cc_final: 0.9062 (m-70) REVERT: A 230 TYR cc_start: 0.8907 (m-10) cc_final: 0.8617 (m-80) REVERT: A 252 ASN cc_start: 0.9427 (m-40) cc_final: 0.9209 (m-40) REVERT: A 258 GLN cc_start: 0.9389 (tp40) cc_final: 0.9031 (mm-40) REVERT: A 312 ARG cc_start: 0.8935 (mmt180) cc_final: 0.8483 (mmm160) REVERT: A 437 GLU cc_start: 0.8921 (pm20) cc_final: 0.8497 (pt0) REVERT: A 448 LYS cc_start: 0.8987 (tptt) cc_final: 0.8668 (tmtt) REVERT: A 470 ASN cc_start: 0.8882 (m110) cc_final: 0.8587 (m110) REVERT: A 481 TYR cc_start: 0.7117 (t80) cc_final: 0.5693 (m-80) REVERT: A 484 MET cc_start: 0.9428 (mtm) cc_final: 0.9032 (mtt) REVERT: A 509 LEU cc_start: 0.7057 (mt) cc_final: 0.6664 (tt) REVERT: A 601 LYS cc_start: 0.9565 (ttmt) cc_final: 0.9304 (mttp) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1982 time to fit residues: 23.9784 Evaluate side-chains 82 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 0.0970 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 41 optimal weight: 0.4980 chunk 35 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.155402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.126681 restraints weight = 16878.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.128763 restraints weight = 14454.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.130526 restraints weight = 12701.957| |-----------------------------------------------------------------------------| r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6375 moved from start: 0.6999 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= 0.173 Angle : 0.758 9.886 5222 Z= 0.381 Chirality : 0.044 0.189 575 Planarity : 0.004 0.047 660 Dihedral : 4.924 20.001 505 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % 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: 0.98 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -4.88 (0.55), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 149 HIS 0.015 0.001 HIS A 479 PHE 0.017 0.001 PHE A 13 TYR 0.024 0.002 TYR A 516 ARG 0.002 0.000 ARG A 496 *********************** 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 104 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.438 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: symmetry clash REVERT: A 37 TYR cc_start: 0.8069 (t80) cc_final: 0.7613 (t80) REVERT: A 144 ASN cc_start: 0.9460 (m-40) cc_final: 0.9058 (m-40) REVERT: A 149 TRP cc_start: 0.8058 (m100) cc_final: 0.7712 (m100) REVERT: A 166 GLU cc_start: 0.9400 (mm-30) cc_final: 0.8988 (mm-30) REVERT: A 209 HIS cc_start: 0.9441 (m90) cc_final: 0.9113 (m-70) REVERT: A 210 ASN cc_start: 0.9432 (t0) cc_final: 0.9054 (t0) REVERT: A 252 ASN cc_start: 0.9435 (m-40) cc_final: 0.9222 (m-40) REVERT: A 258 GLN cc_start: 0.9378 (tp40) cc_final: 0.9048 (mm-40) REVERT: A 312 ARG cc_start: 0.8935 (mmt180) cc_final: 0.8522 (mmm160) REVERT: A 437 GLU cc_start: 0.8888 (pm20) cc_final: 0.8467 (pt0) REVERT: A 448 LYS cc_start: 0.9101 (tptt) cc_final: 0.8510 (tmtt) REVERT: A 484 MET cc_start: 0.9443 (mtm) cc_final: 0.9118 (mtp) REVERT: A 485 MET cc_start: 0.8411 (mmp) cc_final: 0.8005 (mmp) REVERT: A 601 LYS cc_start: 0.9557 (ttmt) cc_final: 0.9291 (mttp) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.2070 time to fit residues: 25.4567 Evaluate side-chains 82 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 ASN A 470 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.143747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.116876 restraints weight = 14320.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.119105 restraints weight = 11985.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.120922 restraints weight = 10344.021| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 moved from start: 0.7950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3881 Z= 0.237 Angle : 0.839 8.148 5222 Z= 0.428 Chirality : 0.046 0.170 575 Planarity : 0.005 0.047 660 Dihedral : 5.345 23.228 505 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % 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: 0.01 (0.39), residues: 445 helix: 0.75 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -4.39 (0.62), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 149 HIS 0.006 0.002 HIS A 401 PHE 0.045 0.003 PHE A 13 TYR 0.029 0.003 TYR A 516 ARG 0.004 0.000 ARG A 450 *********************** 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 101 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.449 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: A 37 TYR cc_start: 0.8326 (t80) cc_final: 0.7778 (t80) REVERT: A 144 ASN cc_start: 0.9522 (m-40) cc_final: 0.9160 (m-40) REVERT: A 149 TRP cc_start: 0.7994 (m100) cc_final: 0.7636 (m100) REVERT: A 173 MET cc_start: 0.9094 (mpp) cc_final: 0.8747 (mpp) REVERT: A 209 HIS cc_start: 0.9436 (m90) cc_final: 0.9077 (m-70) REVERT: A 210 ASN cc_start: 0.9399 (t0) cc_final: 0.9186 (t0) REVERT: A 252 ASN cc_start: 0.9444 (m110) cc_final: 0.9241 (m-40) REVERT: A 258 GLN cc_start: 0.9393 (tp40) cc_final: 0.9064 (mm-40) REVERT: A 271 HIS cc_start: 0.7396 (t-90) cc_final: 0.6769 (m170) REVERT: A 312 ARG cc_start: 0.8940 (mmt180) cc_final: 0.8561 (mmm160) REVERT: A 316 LYS cc_start: 0.9153 (ptpp) cc_final: 0.8731 (ptpp) REVERT: A 437 GLU cc_start: 0.8953 (pm20) cc_final: 0.8596 (pt0) REVERT: A 448 LYS cc_start: 0.9062 (tptt) cc_final: 0.8749 (tmtt) REVERT: A 481 TYR cc_start: 0.7309 (t80) cc_final: 0.6056 (m-80) REVERT: A 484 MET cc_start: 0.9445 (mtm) cc_final: 0.9078 (mtt) REVERT: A 509 LEU cc_start: 0.7323 (mt) cc_final: 0.6847 (tt) REVERT: A 601 LYS cc_start: 0.9615 (ttmt) cc_final: 0.9357 (mttt) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1948 time to fit residues: 23.5041 Evaluate side-chains 85 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 0.0980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.145361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.117561 restraints weight = 14193.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.119870 restraints weight = 11817.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.121774 restraints weight = 10205.471| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 moved from start: 0.8129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3881 Z= 0.202 Angle : 0.814 8.126 5222 Z= 0.417 Chirality : 0.046 0.186 575 Planarity : 0.004 0.047 660 Dihedral : 5.175 20.790 505 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % 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: -0.05 (0.39), residues: 445 helix: 0.70 (0.25), residues: 383 sheet: None (None), residues: 0 loop : -4.47 (0.61), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 6 HIS 0.004 0.001 HIS A 117 PHE 0.046 0.002 PHE A 13 TYR 0.026 0.002 TYR A 576 ARG 0.005 0.000 ARG A 450 ********************** 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 98 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.432 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: A 37 TYR cc_start: 0.8249 (t80) cc_final: 0.7714 (t80) REVERT: A 144 ASN cc_start: 0.9549 (m-40) cc_final: 0.9186 (m-40) REVERT: A 149 TRP cc_start: 0.8121 (m100) cc_final: 0.7815 (m100) REVERT: A 173 MET cc_start: 0.9114 (mpp) cc_final: 0.8764 (mpp) REVERT: A 209 HIS cc_start: 0.9427 (m90) cc_final: 0.9147 (m-70) REVERT: A 210 ASN cc_start: 0.9469 (t0) cc_final: 0.9268 (p0) REVERT: A 252 ASN cc_start: 0.9463 (m110) cc_final: 0.9254 (m-40) REVERT: A 258 GLN cc_start: 0.9382 (tp40) cc_final: 0.9045 (mm-40) REVERT: A 271 HIS cc_start: 0.7208 (t-90) cc_final: 0.6598 (m170) REVERT: A 312 ARG cc_start: 0.8967 (mmt180) cc_final: 0.8043 (mmt180) REVERT: A 316 LYS cc_start: 0.9142 (ptpp) cc_final: 0.8728 (ptpp) REVERT: A 437 GLU cc_start: 0.8903 (pm20) cc_final: 0.8581 (pt0) REVERT: A 446 MET cc_start: 0.8436 (mmm) cc_final: 0.8058 (mmm) REVERT: A 448 LYS cc_start: 0.9081 (tptt) cc_final: 0.8784 (tmtt) REVERT: A 481 TYR cc_start: 0.7363 (t80) cc_final: 0.6230 (m-80) REVERT: A 484 MET cc_start: 0.9441 (mtm) cc_final: 0.9105 (mtt) REVERT: A 509 LEU cc_start: 0.7273 (mt) cc_final: 0.6760 (tt) REVERT: A 601 LYS cc_start: 0.9604 (ttmt) cc_final: 0.9353 (mttp) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.2031 time to fit residues: 23.7313 Evaluate side-chains 87 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 9 optimal weight: 0.3980 chunk 13 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.144611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.119256 restraints weight = 15311.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.121339 restraints weight = 12892.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.123186 restraints weight = 11202.274| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 moved from start: 0.8258 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= 0.187 Angle : 0.791 8.199 5222 Z= 0.403 Chirality : 0.045 0.153 575 Planarity : 0.004 0.047 660 Dihedral : 5.000 19.861 505 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % 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: 0.08 (0.39), residues: 445 helix: 0.79 (0.25), residues: 382 sheet: None (None), residues: 0 loop : -4.38 (0.60), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 149 HIS 0.004 0.001 HIS A 447 PHE 0.035 0.002 PHE A 13 TYR 0.025 0.002 TYR A 516 ARG 0.004 0.000 ARG A 450 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1576.59 seconds wall clock time: 28 minutes 16.14 seconds (1696.14 seconds total)