Starting phenix.real_space_refine on Tue Feb 11 02:44:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zpg_11338/02_2025/6zpg_11338.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zpg_11338/02_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_11338/02_2025/6zpg_11338.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zpg_11338/02_2025/6zpg_11338.map" model { file = "/net/cci-nas-00/data/ceres_data/6zpg_11338/02_2025/6zpg_11338.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zpg_11338/02_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-5592/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: 2.78, per 1000 atoms: 0.73 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: 0.94 Conformation dependent library (CDL) restraints added in 455.4 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: 0.35 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: 1.11 Time building geometry restraints manager: 1.10 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: 0.290 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.470 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.000 ------------------------------------------------------------------------------- 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 : 0.430 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: 0.2473 time to fit residues: 42.4486 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 : 0.448 ------------------------------------------------------------------------------- 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 = 37)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.129900 restraints weight = 15392.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.133082 restraints weight = 11801.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.135453 restraints weight = 9604.476| |-----------------------------------------------------------------------------| r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6117 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 : 0.419 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: 0.1839 (ttt) cc_final: 0.0991 (tmm) REVERT: A 110 GLU cc_start: 0.9111 (tp30) cc_final: 0.8860 (tp30) REVERT: A 111 LEU cc_start: 0.7652 (mp) cc_final: 0.7361 (pp) REVERT: A 115 GLU cc_start: 0.8691 (pt0) cc_final: 0.8441 (pt0) REVERT: A 149 TRP cc_start: 0.7871 (m100) cc_final: 0.7411 (m100) REVERT: A 154 GLU cc_start: 0.8670 (tp30) cc_final: 0.8366 (tm-30) REVERT: A 159 GLN cc_start: 0.8986 (pp30) cc_final: 0.8750 (tm-30) REVERT: A 166 GLU cc_start: 0.9565 (mm-30) cc_final: 0.9208 (mm-30) REVERT: A 210 ASN cc_start: 0.9594 (t0) cc_final: 0.9365 (p0) REVERT: A 252 ASN cc_start: 0.9361 (t0) cc_final: 0.9154 (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: 0.9055 (mm-40) REVERT: A 312 ARG cc_start: 0.8804 (mmt180) cc_final: 0.8502 (mmm160) REVERT: A 440 MET cc_start: 0.9084 (mmt) cc_final: 0.8647 (mmm) REVERT: A 447 HIS cc_start: 0.8785 (p90) cc_final: 0.8436 (p90) REVERT: A 448 LYS cc_start: 0.9053 (tptt) cc_final: 0.8408 (tmtt) REVERT: A 484 MET cc_start: 0.9437 (mtm) cc_final: 0.9118 (mtp) REVERT: A 485 MET cc_start: 0.8550 (mmp) cc_final: 0.8123 (mmp) REVERT: A 580 VAL cc_start: 0.7440 (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: 0.2208 time to fit residues: 29.8324 Evaluate side-chains 91 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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: 2.9990 chunk 15 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4400 r_free = 0.4400 target = 0.159709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.128341 restraints weight = 13892.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.131155 restraints weight = 11153.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.133405 restraints weight = 9473.716| |-----------------------------------------------------------------------------| r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6031 moved from start: 0.4840 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= 0.162 Angle : 0.726 10.356 5222 Z= 0.364 Chirality : 0.041 0.135 575 Planarity : 0.004 0.044 660 Dihedral : 5.013 20.623 505 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % 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: -0.27 (0.39), residues: 445 helix: 0.65 (0.25), residues: 381 sheet: None (None), residues: 0 loop : -5.08 (0.59), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 314 HIS 0.009 0.001 HIS A 447 PHE 0.023 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 108 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 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: 0.2228 (ttt) cc_final: 0.1350 (tmm) REVERT: A 149 TRP cc_start: 0.8100 (m100) cc_final: 0.7698 (m100) REVERT: A 159 GLN cc_start: 0.9156 (pp30) cc_final: 0.8948 (tm-30) REVERT: A 166 GLU cc_start: 0.9565 (mm-30) cc_final: 0.9141 (mm-30) REVERT: A 210 ASN cc_start: 0.9585 (t0) cc_final: 0.9364 (t0) REVERT: A 258 GLN cc_start: 0.9272 (tp40) cc_final: 0.9009 (mm-40) REVERT: A 312 ARG cc_start: 0.8780 (mmt180) cc_final: 0.8457 (mmm160) REVERT: A 316 LYS cc_start: 0.9094 (ptpp) cc_final: 0.8625 (ptpp) REVERT: A 398 LEU cc_start: 0.7864 (tt) cc_final: 0.7567 (mm) REVERT: A 447 HIS cc_start: 0.8823 (p90) cc_final: 0.8606 (p-80) REVERT: A 448 LYS cc_start: 0.9073 (tptt) cc_final: 0.8693 (tmtt) REVERT: A 481 TYR cc_start: 0.7073 (t80) cc_final: 0.4468 (m-80) REVERT: A 484 MET cc_start: 0.9414 (mtm) cc_final: 0.9203 (mtp) REVERT: A 544 MET cc_start: 0.6542 (ptm) cc_final: 0.6330 (ptm) REVERT: A 580 VAL cc_start: 0.7821 (p) cc_final: 0.7421 (t) REVERT: A 601 LYS cc_start: 0.9367 (ttmt) cc_final: 0.9070 (mtpt) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.2082 time to fit residues: 26.4994 Evaluate side-chains 89 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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: 6.9990 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 0.1980 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 100 HIS A 140 GLN A 209 HIS A 470 ASN A 474 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.155728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.123184 restraints weight = 15567.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.125352 restraints weight = 13428.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.127121 restraints weight = 11935.233| |-----------------------------------------------------------------------------| r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6353 moved from start: 0.5736 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= 0.183 Angle : 0.720 8.839 5222 Z= 0.369 Chirality : 0.041 0.146 575 Planarity : 0.005 0.052 660 Dihedral : 4.954 21.589 505 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % 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 (0.39), residues: 445 helix: 0.99 (0.25), residues: 381 sheet: None (None), residues: 0 loop : -5.08 (0.56), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 314 HIS 0.009 0.001 HIS A 447 PHE 0.017 0.002 PHE A 409 TYR 0.025 0.002 TYR A 402 ARG 0.005 0.001 ARG A 496 *********************** 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 106 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 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: symmetry clash REVERT: A 37 TYR cc_start: 0.8176 (t80) cc_final: 0.7743 (t80) REVERT: A 159 GLN cc_start: 0.9001 (pp30) cc_final: 0.8786 (tm-30) REVERT: A 166 GLU cc_start: 0.9516 (mm-30) cc_final: 0.9094 (mm-30) REVERT: A 209 HIS cc_start: 0.9375 (m90) cc_final: 0.9077 (m-70) REVERT: A 210 ASN cc_start: 0.9496 (t0) cc_final: 0.9210 (t0) REVERT: A 258 GLN cc_start: 0.9340 (tp40) cc_final: 0.9062 (mm-40) REVERT: A 316 LYS cc_start: 0.9106 (ptpp) cc_final: 0.8609 (pttm) REVERT: A 448 LYS cc_start: 0.9177 (tptt) cc_final: 0.8631 (tmtt) REVERT: A 481 TYR cc_start: 0.6982 (t80) cc_final: 0.5607 (t80) REVERT: A 484 MET cc_start: 0.9426 (mtm) cc_final: 0.9079 (mmm) REVERT: A 544 MET cc_start: 0.6620 (ptm) cc_final: 0.6418 (ptm) REVERT: A 601 LYS cc_start: 0.9483 (ttmt) cc_final: 0.9153 (mttt) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1944 time to fit residues: 24.5343 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 : 0.396 ------------------------------------------------------------------------------- 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: 0.6980 chunk 11 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.4377 r_free = 0.4377 target = 0.157109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.124481 restraints weight = 16333.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.126737 restraints weight = 14014.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.128538 restraints weight = 12375.728| |-----------------------------------------------------------------------------| r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6300 moved from start: 0.6057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3881 Z= 0.182 Angle : 0.738 8.087 5222 Z= 0.375 Chirality : 0.042 0.149 575 Planarity : 0.004 0.046 660 Dihedral : 4.955 21.161 505 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.25 % Allowed : 1.97 % 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 (0.39), residues: 445 helix: 1.00 (0.25), residues: 383 sheet: None (None), residues: 0 loop : -5.30 (0.51), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 149 HIS 0.008 0.001 HIS A 447 PHE 0.016 0.001 PHE A 409 TYR 0.023 0.002 TYR A 576 ARG 0.004 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: 1 poor density : 105 time to evaluate : 0.412 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: 0.8154 (t80) cc_final: 0.7768 (t80) REVERT: A 115 GLU cc_start: 0.8796 (pt0) cc_final: 0.8573 (pt0) REVERT: A 166 GLU cc_start: 0.9519 (mm-30) cc_final: 0.9072 (mm-30) REVERT: A 209 HIS cc_start: 0.9412 (m90) cc_final: 0.9136 (m-70) REVERT: A 210 ASN cc_start: 0.9526 (t0) cc_final: 0.9294 (t0) REVERT: A 252 ASN cc_start: 0.9460 (m-40) cc_final: 0.9255 (m-40) REVERT: A 258 GLN cc_start: 0.9365 (tp40) cc_final: 0.9065 (mm-40) REVERT: A 312 ARG cc_start: 0.8944 (mmt180) cc_final: 0.8571 (mmm160) REVERT: A 316 LYS cc_start: 0.9127 (ptpp) cc_final: 0.8617 (pttm) REVERT: A 448 LYS cc_start: 0.9133 (tptt) cc_final: 0.8858 (tmtt) REVERT: A 481 TYR cc_start: 0.7198 (t80) cc_final: 0.5189 (m-80) REVERT: A 484 MET cc_start: 0.9409 (mtm) cc_final: 0.9018 (mtp) REVERT: A 509 LEU cc_start: 0.7194 (mt) cc_final: 0.6602 (tt) REVERT: A 544 MET cc_start: 0.6596 (ptm) cc_final: 0.6349 (ptm) REVERT: A 601 LYS cc_start: 0.9473 (ttmt) cc_final: 0.9174 (mttt) outliers start: 1 outliers final: 1 residues processed: 106 average time/residue: 0.1923 time to fit residues: 24.2705 Evaluate side-chains 89 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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: 0.6980 chunk 25 optimal weight: 0.0770 chunk 13 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 470 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.154427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.125094 restraints weight = 14052.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.127504 restraints weight = 11752.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.129465 restraints weight = 10128.359| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6304 moved from start: 0.6295 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 8.225 5222 Z= 0.372 Chirality : 0.042 0.130 575 Planarity : 0.004 0.048 660 Dihedral : 4.905 20.463 505 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.25 % Allowed : 0.49 % 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: 0.24 (0.38), residues: 445 helix: 1.00 (0.25), residues: 383 sheet: None (None), residues: 0 loop : -5.17 (0.51), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 149 HIS 0.008 0.001 HIS A 447 PHE 0.013 0.001 PHE A 409 TYR 0.025 0.002 TYR A 402 ARG 0.003 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 105 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.443 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: 0.8135 (t80) cc_final: 0.7649 (t80) REVERT: A 159 GLN cc_start: 0.8893 (tm-30) cc_final: 0.8592 (tm-30) REVERT: A 209 HIS cc_start: 0.9378 (m90) cc_final: 0.9038 (m-70) REVERT: A 252 ASN cc_start: 0.9414 (m-40) cc_final: 0.9192 (m-40) REVERT: A 258 GLN cc_start: 0.9368 (tp40) cc_final: 0.9069 (mm-40) REVERT: A 312 ARG cc_start: 0.8929 (mmt180) cc_final: 0.8513 (mmm160) REVERT: A 316 LYS cc_start: 0.9032 (ptpp) cc_final: 0.8599 (ptpt) REVERT: A 448 LYS cc_start: 0.9125 (tptt) cc_final: 0.8584 (tmtt) REVERT: A 481 TYR cc_start: 0.6991 (t80) cc_final: 0.5417 (t80) REVERT: A 484 MET cc_start: 0.9458 (mtm) cc_final: 0.9099 (mtm) REVERT: A 544 MET cc_start: 0.6546 (ptm) cc_final: 0.6271 (ptm) outliers start: 1 outliers final: 1 residues processed: 105 average time/residue: 0.2030 time to fit residues: 25.3351 Evaluate side-chains 84 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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: 4.9990 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.136340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.112094 restraints weight = 16366.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.114030 restraints weight = 13304.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.116252 restraints weight = 11442.686| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.7820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 3881 Z= 0.325 Angle : 0.902 9.657 5222 Z= 0.477 Chirality : 0.048 0.224 575 Planarity : 0.006 0.077 660 Dihedral : 5.566 25.322 505 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 23.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.25 % Allowed : 2.70 % 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: -0.42 (0.38), residues: 445 helix: 0.49 (0.25), residues: 381 sheet: None (None), residues: 0 loop : -4.80 (0.55), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 149 HIS 0.008 0.002 HIS A 447 PHE 0.028 0.003 PHE A 409 TYR 0.037 0.003 TYR A 33 ARG 0.005 0.001 ARG A 126 *********************** 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 109 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.400 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 33 TYR cc_start: 0.3875 (OUTLIER) cc_final: 0.0247 (m-10) REVERT: A 144 ASN cc_start: 0.9477 (m-40) cc_final: 0.9238 (m-40) REVERT: A 149 TRP cc_start: 0.7721 (m100) cc_final: 0.7355 (m100) REVERT: A 159 GLN cc_start: 0.9043 (tm-30) cc_final: 0.8763 (tm-30) REVERT: A 166 GLU cc_start: 0.9420 (mm-30) cc_final: 0.8929 (mm-30) REVERT: A 209 HIS cc_start: 0.9389 (m90) cc_final: 0.9086 (m-70) REVERT: A 210 ASN cc_start: 0.9366 (t0) cc_final: 0.9020 (t0) REVERT: A 252 ASN cc_start: 0.9477 (m110) cc_final: 0.9239 (m110) REVERT: A 258 GLN cc_start: 0.9385 (tp40) cc_final: 0.9017 (mm-40) REVERT: A 271 HIS cc_start: 0.7414 (t-90) cc_final: 0.6760 (m90) REVERT: A 312 ARG cc_start: 0.9001 (mmt180) cc_final: 0.7902 (ptp-170) REVERT: A 316 LYS cc_start: 0.9158 (ptpp) cc_final: 0.8654 (ptpp) REVERT: A 437 GLU cc_start: 0.8880 (pm20) cc_final: 0.8480 (pt0) REVERT: A 448 LYS cc_start: 0.9183 (tptt) cc_final: 0.8932 (tmtt) REVERT: A 481 TYR cc_start: 0.7344 (t80) cc_final: 0.5947 (m-80) REVERT: A 484 MET cc_start: 0.9399 (mtm) cc_final: 0.8967 (mtp) REVERT: A 509 LEU cc_start: 0.7527 (mt) cc_final: 0.7063 (tt) REVERT: A 544 MET cc_start: 0.7031 (ptm) cc_final: 0.6744 (ptm) REVERT: A 601 LYS cc_start: 0.9591 (ttmt) cc_final: 0.9379 (mmtm) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.1940 time to fit residues: 25.1199 Evaluate side-chains 93 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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: 0.9990 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 41 optimal weight: 0.4980 chunk 35 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.4228 r_free = 0.4228 target = 0.142869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.115728 restraints weight = 16779.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.118167 restraints weight = 13994.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.120257 restraints weight = 12005.928| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6456 moved from start: 0.7768 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= 0.191 Angle : 0.797 7.341 5222 Z= 0.402 Chirality : 0.045 0.142 575 Planarity : 0.004 0.047 660 Dihedral : 5.229 20.281 505 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % 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: -0.06 (0.38), residues: 445 helix: 0.72 (0.25), residues: 383 sheet: None (None), residues: 0 loop : -4.66 (0.56), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 149 HIS 0.010 0.001 HIS A 479 PHE 0.023 0.002 PHE A 13 TYR 0.030 0.002 TYR A 516 ARG 0.003 0.000 ARG A 549 *********************** 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 107 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 ASN cc_start: 0.9506 (m-40) cc_final: 0.9248 (m-40) REVERT: A 149 TRP cc_start: 0.8068 (m100) cc_final: 0.7649 (m100) REVERT: A 159 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8574 (tm-30) REVERT: A 209 HIS cc_start: 0.9445 (m90) cc_final: 0.9196 (m-70) REVERT: A 210 ASN cc_start: 0.9475 (t0) cc_final: 0.9238 (p0) REVERT: A 252 ASN cc_start: 0.9367 (m110) cc_final: 0.9160 (m110) REVERT: A 258 GLN cc_start: 0.9364 (tp40) cc_final: 0.9049 (mm-40) REVERT: A 271 HIS cc_start: 0.7064 (t-90) cc_final: 0.6436 (m170) REVERT: A 312 ARG cc_start: 0.8954 (mmt180) cc_final: 0.8538 (mmm160) REVERT: A 316 LYS cc_start: 0.9148 (ptpp) cc_final: 0.8652 (ptpp) REVERT: A 437 GLU cc_start: 0.8979 (pm20) cc_final: 0.8589 (pt0) REVERT: A 448 LYS cc_start: 0.9248 (tptt) cc_final: 0.8701 (tmtt) REVERT: A 481 TYR cc_start: 0.7391 (t80) cc_final: 0.6155 (t80) REVERT: A 484 MET cc_start: 0.9415 (mtm) cc_final: 0.9144 (mtt) REVERT: A 544 MET cc_start: 0.6536 (ptm) cc_final: 0.6329 (ptm) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1913 time to fit residues: 24.6387 Evaluate side-chains 94 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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: 0.9990 chunk 3 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 44 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.4175 r_free = 0.4175 target = 0.139780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.115194 restraints weight = 16324.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.117738 restraints weight = 13211.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.119761 restraints weight = 11049.857| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.8278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3881 Z= 0.231 Angle : 0.823 7.793 5222 Z= 0.426 Chirality : 0.045 0.184 575 Planarity : 0.005 0.048 660 Dihedral : 5.365 22.574 505 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 19.28 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: -0.06 (0.39), residues: 445 helix: 0.68 (0.25), residues: 382 sheet: None (None), residues: 0 loop : -4.30 (0.61), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 149 HIS 0.013 0.001 HIS A 447 PHE 0.051 0.002 PHE A 13 TYR 0.027 0.002 TYR A 576 ARG 0.003 0.000 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 105 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.435 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 144 ASN cc_start: 0.9585 (m-40) cc_final: 0.9318 (m-40) REVERT: A 149 TRP cc_start: 0.7942 (m100) cc_final: 0.7592 (m100) REVERT: A 159 GLN cc_start: 0.8884 (tm-30) cc_final: 0.8564 (tm-30) REVERT: A 173 MET cc_start: 0.9190 (mpp) cc_final: 0.8828 (mpp) REVERT: A 209 HIS cc_start: 0.9443 (m90) cc_final: 0.9094 (m-70) REVERT: A 210 ASN cc_start: 0.9397 (t0) cc_final: 0.9128 (t0) REVERT: A 252 ASN cc_start: 0.9328 (m110) cc_final: 0.9108 (m110) REVERT: A 258 GLN cc_start: 0.9350 (tp40) cc_final: 0.9045 (mm-40) REVERT: A 271 HIS cc_start: 0.7216 (t-90) cc_final: 0.6594 (m90) REVERT: A 312 ARG cc_start: 0.8993 (mmt180) cc_final: 0.7948 (mmt180) REVERT: A 316 LYS cc_start: 0.9134 (ptpp) cc_final: 0.8607 (ptpp) REVERT: A 437 GLU cc_start: 0.8921 (pm20) cc_final: 0.8589 (pt0) REVERT: A 448 LYS cc_start: 0.9141 (tptt) cc_final: 0.8857 (tmtt) REVERT: A 481 TYR cc_start: 0.7148 (t80) cc_final: 0.5815 (m-80) REVERT: A 484 MET cc_start: 0.9430 (mtm) cc_final: 0.8956 (mtt) REVERT: A 509 LEU cc_start: 0.7387 (mt) cc_final: 0.6907 (tt) REVERT: A 544 MET cc_start: 0.6696 (ptm) cc_final: 0.6462 (ptm) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2075 time to fit residues: 26.1324 Evaluate side-chains 88 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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: 0.8980 chunk 20 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 chunk 12 optimal weight: 0.3980 chunk 44 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 0.0060 chunk 6 optimal weight: 2.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.141413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.115439 restraints weight = 16376.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.118011 restraints weight = 13444.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.120123 restraints weight = 11382.705| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.8470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3881 Z= 0.229 Angle : 0.856 9.405 5222 Z= 0.444 Chirality : 0.047 0.169 575 Planarity : 0.004 0.048 660 Dihedral : 5.174 19.621 505 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 16.14 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: -0.26 (0.38), residues: 445 helix: 0.49 (0.25), residues: 385 sheet: None (None), residues: 0 loop : -4.16 (0.62), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 149 HIS 0.015 0.001 HIS A 447 PHE 0.042 0.002 PHE A 13 TYR 0.038 0.002 TYR A 516 ARG 0.002 0.000 ARG A 306 ********************** 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 102 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.437 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 12 LYS cc_start: 0.8614 (mmpt) cc_final: 0.8403 (mmmt) REVERT: A 37 TYR cc_start: 0.8311 (t80) cc_final: 0.7813 (t80) REVERT: A 144 ASN cc_start: 0.9609 (m-40) cc_final: 0.9351 (m-40) REVERT: A 149 TRP cc_start: 0.8094 (m100) cc_final: 0.7681 (m100) REVERT: A 159 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8579 (tm-30) REVERT: A 173 MET cc_start: 0.9093 (mpp) cc_final: 0.8717 (mpp) REVERT: A 209 HIS cc_start: 0.9431 (m90) cc_final: 0.9163 (m-70) REVERT: A 210 ASN cc_start: 0.9455 (t0) cc_final: 0.9217 (p0) REVERT: A 252 ASN cc_start: 0.9313 (m110) cc_final: 0.9092 (m-40) REVERT: A 258 GLN cc_start: 0.9351 (tp40) cc_final: 0.9045 (mm-40) REVERT: A 312 ARG cc_start: 0.8959 (mmt180) cc_final: 0.8010 (mmm160) REVERT: A 316 LYS cc_start: 0.9104 (ptpp) cc_final: 0.8581 (ptpp) REVERT: A 398 LEU cc_start: 0.8717 (pp) cc_final: 0.8481 (tp) REVERT: A 437 GLU cc_start: 0.8932 (pm20) cc_final: 0.8557 (pt0) REVERT: A 448 LYS cc_start: 0.9166 (tptt) cc_final: 0.8805 (tmtt) REVERT: A 509 LEU cc_start: 0.6864 (mt) cc_final: 0.6627 (tt) REVERT: A 544 MET cc_start: 0.6436 (ptm) cc_final: 0.6228 (ptm) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1984 time to fit residues: 24.1431 Evaluate side-chains 91 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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: 2.9990 chunk 13 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.4158 r_free = 0.4158 target = 0.137899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.113566 restraints weight = 16051.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.116034 restraints weight = 12914.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.118021 restraints weight = 10787.468| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.8915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3881 Z= 0.231 Angle : 0.836 8.084 5222 Z= 0.440 Chirality : 0.046 0.180 575 Planarity : 0.005 0.047 660 Dihedral : 5.240 22.700 505 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % 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: -0.13 (0.38), residues: 445 helix: 0.62 (0.25), residues: 382 sheet: None (None), residues: 0 loop : -4.20 (0.63), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 149 HIS 0.014 0.002 HIS A 447 PHE 0.041 0.002 PHE A 13 TYR 0.027 0.002 TYR A 576 ARG 0.003 0.000 ARG A 393 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1533.85 seconds wall clock time: 28 minutes 15.25 seconds (1695.25 seconds total)