Starting phenix.real_space_refine on Tue Mar 3 12:02:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zpg_11338/03_2026/6zpg_11338.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zpg_11338/03_2026/6zpg_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_2026/6zpg_11338.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zpg_11338/03_2026/6zpg_11338.map" model { file = "/net/cci-nas-00/data/ceres_data/6zpg_11338/03_2026/6zpg_11338.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zpg_11338/03_2026/6zpg_11338.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.00, per 1000 atoms: 0.26 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: 0.30 Conformation dependent library (CDL) restraints added in 142.0 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: 0.20 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: 0.55 Time building geometry restraints manager: 0.41 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: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.840 Find NCS groups from input model: 0.020 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.600 ------------------------------------------------------------------------------- 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= 0.227 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.001 0.000 ARG A 127 TYR 0.015 0.001 TYR A 576 PHE 0.011 0.001 PHE A 409 TRP 0.010 0.002 TRP A 314 HIS 0.013 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 3881) covalent geometry : angle 0.98701 ( 5222) hydrogen bonds : bond 0.08038 ( 309) hydrogen bonds : angle 5.63217 ( 927) *********************** 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 : 0.172 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: 0.5911 (m-10) REVERT: A 37 TYR cc_start: 0.7503 (t80) cc_final: 0.6807 (t80) REVERT: A 154 GLU cc_start: 0.8716 (tp30) cc_final: 0.8200 (mm-30) REVERT: A 166 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8737 (mm-30) REVERT: A 210 ASN cc_start: 0.8752 (t0) cc_final: 0.8531 (t0) REVERT: A 223 MET cc_start: 0.7213 (mmm) cc_final: 0.6827 (mmm) REVERT: A 312 ARG cc_start: 0.8687 (mmt180) cc_final: 0.8024 (ptp-170) REVERT: A 322 MET cc_start: 0.8861 (mmt) cc_final: 0.8569 (tpp) REVERT: A 448 LYS cc_start: 0.8720 (tptt) cc_final: 0.8392 (ptmm) REVERT: A 481 TYR cc_start: 0.6252 (t80) cc_final: 0.4503 (m-80) REVERT: A 484 MET cc_start: 0.9002 (mtm) cc_final: 0.8656 (mtp) REVERT: A 580 VAL cc_start: 0.7152 (p) cc_final: 0.6706 (t) outliers start: 1 outliers final: 1 residues processed: 150 average time/residue: 0.1085 time to fit residues: 18.6487 Evaluate side-chains 97 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.0170 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.157274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.128254 restraints weight = 15547.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.131387 restraints weight = 12282.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.133622 restraints weight = 10144.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.135695 restraints weight = 8743.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.137337 restraints weight = 7613.482| |-----------------------------------------------------------------------------| r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6102 moved from start: 0.4229 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= 0.143 Angle : 0.740 9.558 5222 Z= 0.373 Chirality : 0.040 0.140 575 Planarity : 0.005 0.044 660 Dihedral : 5.282 22.705 505 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.25 % Allowed : 4.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.37), 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 ARG 0.007 0.001 ARG A 496 TYR 0.022 0.002 TYR A 516 PHE 0.006 0.001 PHE A 410 TRP 0.005 0.001 TRP A 314 HIS 0.011 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 3881) covalent geometry : angle 0.74036 ( 5222) hydrogen bonds : bond 0.04293 ( 309) hydrogen bonds : angle 4.71745 ( 927) *********************** 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 117 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.139 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: 0.1871 (ttt) cc_final: 0.1008 (tmm) REVERT: A 110 GLU cc_start: 0.9046 (tp30) cc_final: 0.8816 (tp30) REVERT: A 149 TRP cc_start: 0.7786 (m100) cc_final: 0.7314 (m100) REVERT: A 154 GLU cc_start: 0.8673 (tp30) cc_final: 0.8412 (mm-30) REVERT: A 159 GLN cc_start: 0.8920 (pp30) cc_final: 0.8630 (tm-30) REVERT: A 166 GLU cc_start: 0.9527 (mm-30) cc_final: 0.9199 (mm-30) REVERT: A 256 LEU cc_start: 0.9482 (mm) cc_final: 0.8926 (mm) REVERT: A 258 GLN cc_start: 0.9299 (tp40) cc_final: 0.9063 (mm-40) REVERT: A 260 TYR cc_start: 0.9592 (m-10) cc_final: 0.9369 (m-10) REVERT: A 312 ARG cc_start: 0.8827 (mmt180) cc_final: 0.8494 (mmm160) REVERT: A 440 MET cc_start: 0.9072 (mmt) cc_final: 0.8661 (mmm) REVERT: A 447 HIS cc_start: 0.8758 (p90) cc_final: 0.8509 (p90) REVERT: A 448 LYS cc_start: 0.9004 (tptt) cc_final: 0.8338 (tmtt) REVERT: A 475 PHE cc_start: 0.8724 (t80) cc_final: 0.8515 (t80) REVERT: A 484 MET cc_start: 0.9430 (mtm) cc_final: 0.9096 (mtp) REVERT: A 485 MET cc_start: 0.8485 (mmp) cc_final: 0.8080 (mmp) REVERT: A 580 VAL cc_start: 0.7365 (p) cc_final: 0.6852 (t) outliers start: 1 outliers final: 1 residues processed: 116 average time/residue: 0.0872 time to fit residues: 11.9576 Evaluate side-chains 83 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 29 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 232 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.159203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.127730 restraints weight = 14150.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.130843 restraints weight = 11200.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.133299 restraints weight = 9246.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.135094 restraints weight = 7897.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.136796 restraints weight = 6959.964| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5936 moved from start: 0.4984 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= 0.138 Angle : 0.723 10.038 5222 Z= 0.366 Chirality : 0.041 0.137 575 Planarity : 0.005 0.044 660 Dihedral : 5.015 20.710 505 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.39), residues: 445 helix: 0.61 (0.25), residues: 380 sheet: None (None), residues: 0 loop : -5.08 (0.60), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 496 TYR 0.023 0.002 TYR A 576 PHE 0.022 0.002 PHE A 410 TRP 0.004 0.001 TRP A 149 HIS 0.010 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 3881) covalent geometry : angle 0.72326 ( 5222) hydrogen bonds : bond 0.04165 ( 309) hydrogen bonds : angle 4.67575 ( 927) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.191 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 1 MET cc_start: 0.2161 (ttt) cc_final: 0.1310 (tmm) REVERT: A 166 GLU cc_start: 0.9590 (mm-30) cc_final: 0.9294 (mm-30) REVERT: A 312 ARG cc_start: 0.8745 (mmt180) cc_final: 0.8435 (mmm160) REVERT: A 326 GLN cc_start: 0.9029 (pp30) cc_final: 0.8813 (pp30) REVERT: A 398 LEU cc_start: 0.7839 (tt) cc_final: 0.7554 (mm) REVERT: A 447 HIS cc_start: 0.8832 (p90) cc_final: 0.8583 (p-80) REVERT: A 448 LYS cc_start: 0.9060 (tptt) cc_final: 0.8694 (tmtt) REVERT: A 481 TYR cc_start: 0.7012 (t80) cc_final: 0.4704 (m-80) REVERT: A 484 MET cc_start: 0.9400 (mtm) cc_final: 0.9086 (mtp) REVERT: A 509 LEU cc_start: 0.6783 (mt) cc_final: 0.6238 (tt) REVERT: A 544 MET cc_start: 0.6279 (ptm) cc_final: 0.6070 (ptm) REVERT: A 580 VAL cc_start: 0.7777 (p) cc_final: 0.7411 (t) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.0847 time to fit residues: 10.5946 Evaluate side-chains 83 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 29 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 34 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 GLN 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 = 0.4332 r_free = 0.4332 target = 0.151999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.120742 restraints weight = 14705.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.123580 restraints weight = 11866.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.125459 restraints weight = 9985.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.127446 restraints weight = 8782.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.128948 restraints weight = 7801.674| |-----------------------------------------------------------------------------| r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6102 moved from start: 0.6136 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= 0.164 Angle : 0.774 10.163 5222 Z= 0.391 Chirality : 0.042 0.148 575 Planarity : 0.005 0.051 660 Dihedral : 5.037 21.984 505 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.39), residues: 445 helix: 0.85 (0.25), residues: 382 sheet: None (None), residues: 0 loop : -5.27 (0.51), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 496 TYR 0.031 0.002 TYR A 402 PHE 0.012 0.001 PHE A 475 TRP 0.009 0.002 TRP A 149 HIS 0.009 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 3881) covalent geometry : angle 0.77428 ( 5222) hydrogen bonds : bond 0.04356 ( 309) hydrogen bonds : angle 4.68551 ( 927) *********************** 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 95 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.087 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 209 HIS cc_start: 0.9397 (m90) cc_final: 0.9149 (m-70) REVERT: A 258 GLN cc_start: 0.9230 (mm-40) cc_final: 0.8849 (mm-40) REVERT: A 312 ARG cc_start: 0.8890 (mmt180) cc_final: 0.8540 (mmm160) REVERT: A 316 LYS cc_start: 0.9178 (ptpp) cc_final: 0.8783 (pttm) REVERT: A 448 LYS cc_start: 0.9180 (tptt) cc_final: 0.8770 (tmtt) REVERT: A 481 TYR cc_start: 0.7151 (t80) cc_final: 0.5394 (t80) REVERT: A 484 MET cc_start: 0.9387 (mtm) cc_final: 0.9066 (mtt) REVERT: A 544 MET cc_start: 0.6544 (ptm) cc_final: 0.6331 (ptm) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.0825 time to fit residues: 9.3923 Evaluate side-chains 71 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 14 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.147104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.120540 restraints weight = 15652.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.122907 restraints weight = 13180.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.124911 restraints weight = 11366.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.126396 restraints weight = 9991.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.127772 restraints weight = 8968.230| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6321 moved from start: 0.6660 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= 0.146 Angle : 0.749 7.566 5222 Z= 0.379 Chirality : 0.042 0.128 575 Planarity : 0.004 0.046 660 Dihedral : 5.021 21.095 505 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.38), residues: 445 helix: 0.89 (0.25), residues: 382 sheet: None (None), residues: 0 loop : -5.06 (0.51), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 549 TYR 0.025 0.002 TYR A 576 PHE 0.016 0.001 PHE A 409 TRP 0.009 0.002 TRP A 149 HIS 0.008 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 3881) covalent geometry : angle 0.74911 ( 5222) hydrogen bonds : bond 0.04199 ( 309) hydrogen bonds : angle 4.62512 ( 927) *********************** 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 101 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8145 (t80) cc_final: 0.7548 (t80) REVERT: A 149 TRP cc_start: 0.7395 (m-90) cc_final: 0.6983 (m-90) REVERT: A 163 GLU cc_start: 0.9012 (pt0) cc_final: 0.8686 (pt0) REVERT: A 209 HIS cc_start: 0.9393 (m90) cc_final: 0.9027 (m-70) REVERT: A 256 LEU cc_start: 0.9333 (mm) cc_final: 0.9006 (mm) REVERT: A 258 GLN cc_start: 0.9365 (mm-40) cc_final: 0.8829 (mm-40) REVERT: A 312 ARG cc_start: 0.8926 (mmt180) cc_final: 0.8500 (mmm160) REVERT: A 316 LYS cc_start: 0.9080 (ptpp) cc_final: 0.8599 (ptpt) REVERT: A 402 TYR cc_start: 0.7761 (m-80) cc_final: 0.7301 (m-80) REVERT: A 437 GLU cc_start: 0.8879 (pm20) cc_final: 0.8480 (pt0) REVERT: A 448 LYS cc_start: 0.9037 (tptt) cc_final: 0.8742 (tmtt) REVERT: A 470 ASN cc_start: 0.8937 (m110) cc_final: 0.8633 (m-40) REVERT: A 475 PHE cc_start: 0.9175 (t80) cc_final: 0.8901 (t80) REVERT: A 481 TYR cc_start: 0.7099 (t80) cc_final: 0.5937 (m-80) REVERT: A 483 ASP cc_start: 0.9493 (t70) cc_final: 0.9277 (t0) REVERT: A 484 MET cc_start: 0.9444 (mtm) cc_final: 0.9223 (mmp) REVERT: A 509 LEU cc_start: 0.6879 (mt) cc_final: 0.6676 (tt) REVERT: A 544 MET cc_start: 0.6561 (ptm) cc_final: 0.6263 (ptm) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.0819 time to fit residues: 9.9099 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 : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 9 optimal weight: 0.0870 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- 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 470 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.144677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.119734 restraints weight = 15601.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.122243 restraints weight = 12447.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.124357 restraints weight = 10361.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.126074 restraints weight = 8869.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.127411 restraints weight = 7735.049| |-----------------------------------------------------------------------------| r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 moved from start: 0.7119 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= 0.147 Angle : 0.768 9.669 5222 Z= 0.379 Chirality : 0.042 0.126 575 Planarity : 0.004 0.048 660 Dihedral : 4.967 21.876 505 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.38), residues: 445 helix: 0.99 (0.25), residues: 380 sheet: None (None), residues: 0 loop : -4.89 (0.52), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 549 TYR 0.027 0.002 TYR A 516 PHE 0.015 0.001 PHE A 409 TRP 0.013 0.002 TRP A 149 HIS 0.008 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 3881) covalent geometry : angle 0.76821 ( 5222) hydrogen bonds : bond 0.04248 ( 309) hydrogen bonds : angle 4.53335 ( 927) *********************** 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 97 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.086 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: 0.8157 (t80) cc_final: 0.7565 (t80) REVERT: A 209 HIS cc_start: 0.9385 (m90) cc_final: 0.9029 (m-70) REVERT: A 252 ASN cc_start: 0.9457 (m-40) cc_final: 0.9229 (m110) REVERT: A 258 GLN cc_start: 0.9398 (mm-40) cc_final: 0.8784 (mm-40) REVERT: A 271 HIS cc_start: 0.7226 (t-90) cc_final: 0.6609 (m170) REVERT: A 312 ARG cc_start: 0.8931 (mmt180) cc_final: 0.8471 (mmm160) REVERT: A 398 LEU cc_start: 0.8449 (tt) cc_final: 0.8133 (mm) REVERT: A 437 GLU cc_start: 0.8837 (pm20) cc_final: 0.8452 (pt0) REVERT: A 448 LYS cc_start: 0.9108 (tptt) cc_final: 0.8584 (tmtt) REVERT: A 481 TYR cc_start: 0.7124 (t80) cc_final: 0.5763 (t80) REVERT: A 484 MET cc_start: 0.9435 (mtm) cc_final: 0.9114 (mtt) REVERT: A 544 MET cc_start: 0.6408 (ptm) cc_final: 0.6195 (ptm) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.0770 time to fit residues: 9.0138 Evaluate side-chains 79 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 9 optimal weight: 0.6980 chunk 31 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 16 optimal weight: 0.3980 chunk 7 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 140 GLN A 144 ASN A 470 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.147307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.121794 restraints weight = 19722.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.123729 restraints weight = 17016.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.124975 restraints weight = 14986.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.126535 restraints weight = 13590.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.127652 restraints weight = 12370.666| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 moved from start: 0.7453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3881 Z= 0.158 Angle : 0.798 8.310 5222 Z= 0.403 Chirality : 0.044 0.160 575 Planarity : 0.004 0.048 660 Dihedral : 5.051 21.809 505 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.38), residues: 445 helix: 0.89 (0.25), residues: 381 sheet: None (None), residues: 0 loop : -4.61 (0.56), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 549 TYR 0.023 0.002 TYR A 576 PHE 0.015 0.001 PHE A 409 TRP 0.012 0.002 TRP A 149 HIS 0.008 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 3881) covalent geometry : angle 0.79838 ( 5222) hydrogen bonds : bond 0.04287 ( 309) hydrogen bonds : angle 4.67183 ( 927) *********************** 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 101 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.154 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: 0.8407 (t80) cc_final: 0.7908 (t80) REVERT: A 149 TRP cc_start: 0.7931 (m-90) cc_final: 0.7519 (m-90) REVERT: A 209 HIS cc_start: 0.9464 (m90) cc_final: 0.9117 (m-70) REVERT: A 271 HIS cc_start: 0.7131 (t-90) cc_final: 0.6523 (m170) REVERT: A 312 ARG cc_start: 0.8917 (mmt180) cc_final: 0.8107 (mmm160) REVERT: A 437 GLU cc_start: 0.9108 (pm20) cc_final: 0.8686 (pt0) REVERT: A 448 LYS cc_start: 0.9181 (tptt) cc_final: 0.8943 (tmtt) REVERT: A 470 ASN cc_start: 0.8903 (m110) cc_final: 0.8681 (m-40) REVERT: A 481 TYR cc_start: 0.7193 (t80) cc_final: 0.5662 (m-80) REVERT: A 484 MET cc_start: 0.9404 (mtm) cc_final: 0.9011 (mtp) REVERT: A 509 LEU cc_start: 0.7268 (mt) cc_final: 0.6741 (tt) REVERT: A 544 MET cc_start: 0.6313 (ptm) cc_final: 0.6053 (ptm) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.0810 time to fit residues: 9.7765 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 : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 14 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS A 470 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.147232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.120131 restraints weight = 15253.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.122831 restraints weight = 11981.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.124933 restraints weight = 9903.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.126741 restraints weight = 8468.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.128186 restraints weight = 7409.945| |-----------------------------------------------------------------------------| r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 moved from start: 0.7690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3881 Z= 0.141 Angle : 0.778 7.923 5222 Z= 0.387 Chirality : 0.044 0.136 575 Planarity : 0.004 0.048 660 Dihedral : 4.980 20.556 505 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.38), residues: 445 helix: 0.96 (0.25), residues: 380 sheet: None (None), residues: 0 loop : -4.50 (0.57), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 549 TYR 0.025 0.002 TYR A 516 PHE 0.026 0.002 PHE A 13 TRP 0.022 0.002 TRP A 149 HIS 0.013 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 3881) covalent geometry : angle 0.77773 ( 5222) hydrogen bonds : bond 0.04250 ( 309) hydrogen bonds : angle 4.57022 ( 927) *********************** 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 98 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.160 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 209 HIS cc_start: 0.9424 (m90) cc_final: 0.9066 (m-70) REVERT: A 252 ASN cc_start: 0.9506 (m-40) cc_final: 0.9281 (m-40) REVERT: A 271 HIS cc_start: 0.7128 (t-90) cc_final: 0.6469 (m170) REVERT: A 312 ARG cc_start: 0.8902 (mmt180) cc_final: 0.8127 (mmm160) REVERT: A 437 GLU cc_start: 0.8993 (pm20) cc_final: 0.8535 (pt0) REVERT: A 448 LYS cc_start: 0.9152 (tptt) cc_final: 0.8545 (tmtt) REVERT: A 470 ASN cc_start: 0.8753 (m-40) cc_final: 0.8508 (m110) REVERT: A 481 TYR cc_start: 0.7306 (t80) cc_final: 0.6136 (t80) REVERT: A 484 MET cc_start: 0.9430 (mtm) cc_final: 0.9097 (mtt) REVERT: A 544 MET cc_start: 0.6262 (ptm) cc_final: 0.6018 (ptm) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.0713 time to fit residues: 8.5054 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 : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.145366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.120080 restraints weight = 15350.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.122416 restraints weight = 12775.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.124313 restraints weight = 10924.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.125825 restraints weight = 9555.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.127086 restraints weight = 8510.620| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.7814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3881 Z= 0.137 Angle : 0.772 7.843 5222 Z= 0.383 Chirality : 0.044 0.163 575 Planarity : 0.004 0.050 660 Dihedral : 5.001 20.350 505 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 15.35 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.38), residues: 445 helix: 0.99 (0.25), residues: 381 sheet: None (None), residues: 0 loop : -4.40 (0.61), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 450 TYR 0.024 0.002 TYR A 576 PHE 0.048 0.002 PHE A 13 TRP 0.020 0.002 TRP A 149 HIS 0.014 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 3881) covalent geometry : angle 0.77170 ( 5222) hydrogen bonds : bond 0.04095 ( 309) hydrogen bonds : angle 4.51904 ( 927) *********************** 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 98 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.7993 (t80) cc_final: 0.7431 (t80) REVERT: A 209 HIS cc_start: 0.9376 (m90) cc_final: 0.9034 (m-70) REVERT: A 252 ASN cc_start: 0.9499 (m-40) cc_final: 0.9264 (m-40) REVERT: A 267 MET cc_start: 0.7328 (mmm) cc_final: 0.5902 (ttm) REVERT: A 271 HIS cc_start: 0.7066 (t-90) cc_final: 0.6417 (m170) REVERT: A 312 ARG cc_start: 0.8870 (mmt180) cc_final: 0.7990 (mmm160) REVERT: A 402 TYR cc_start: 0.7847 (m-80) cc_final: 0.7636 (m-80) REVERT: A 437 GLU cc_start: 0.8860 (pm20) cc_final: 0.8462 (pt0) REVERT: A 446 MET cc_start: 0.8603 (tpp) cc_final: 0.8341 (mmm) REVERT: A 448 LYS cc_start: 0.9051 (tptt) cc_final: 0.8710 (tmtt) REVERT: A 470 ASN cc_start: 0.8911 (m-40) cc_final: 0.8631 (m-40) REVERT: A 481 TYR cc_start: 0.7143 (t80) cc_final: 0.5659 (m-80) REVERT: A 484 MET cc_start: 0.9429 (mtm) cc_final: 0.8951 (mtt) REVERT: A 509 LEU cc_start: 0.7126 (mt) cc_final: 0.6735 (tt) REVERT: A 544 MET cc_start: 0.6128 (ptm) cc_final: 0.5894 (ptm) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.0778 time to fit residues: 9.2209 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 : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 40 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 45 optimal weight: 0.0980 chunk 4 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 568 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.146590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.120300 restraints weight = 15358.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.122787 restraints weight = 12853.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.124688 restraints weight = 11023.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.126330 restraints weight = 9642.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.127700 restraints weight = 8585.617| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6338 moved from start: 0.8068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3881 Z= 0.152 Angle : 0.804 9.223 5222 Z= 0.401 Chirality : 0.045 0.141 575 Planarity : 0.004 0.048 660 Dihedral : 4.977 20.104 505 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.38), residues: 445 helix: 0.78 (0.25), residues: 385 sheet: None (None), residues: 0 loop : -4.29 (0.63), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 549 TYR 0.025 0.002 TYR A 516 PHE 0.042 0.002 PHE A 13 TRP 0.021 0.002 TRP A 149 HIS 0.014 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 3881) covalent geometry : angle 0.80429 ( 5222) hydrogen bonds : bond 0.04265 ( 309) hydrogen bonds : angle 4.69725 ( 927) ********************** 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 99 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.151 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 12 LYS cc_start: 0.8541 (mmpt) cc_final: 0.8315 (mmmt) REVERT: A 37 TYR cc_start: 0.7990 (t80) cc_final: 0.7425 (t80) REVERT: A 205 LYS cc_start: 0.9543 (mtmm) cc_final: 0.9330 (ptpt) REVERT: A 209 HIS cc_start: 0.9416 (m90) cc_final: 0.9026 (m-70) REVERT: A 252 ASN cc_start: 0.9445 (m-40) cc_final: 0.9205 (m-40) REVERT: A 267 MET cc_start: 0.7333 (mmm) cc_final: 0.5924 (ttm) REVERT: A 271 HIS cc_start: 0.7055 (t-90) cc_final: 0.6415 (m170) REVERT: A 312 ARG cc_start: 0.8769 (mmt180) cc_final: 0.8440 (mmm160) REVERT: A 437 GLU cc_start: 0.8860 (pm20) cc_final: 0.8487 (pt0) REVERT: A 448 LYS cc_start: 0.9088 (tptt) cc_final: 0.8732 (tmtt) REVERT: A 470 ASN cc_start: 0.8795 (m-40) cc_final: 0.8505 (m-40) REVERT: A 484 MET cc_start: 0.9448 (mtm) cc_final: 0.9236 (mtt) REVERT: A 509 LEU cc_start: 0.6829 (mt) cc_final: 0.6566 (tt) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.0740 time to fit residues: 8.8770 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 : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 22 optimal weight: 0.0070 chunk 3 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 9 optimal weight: 0.0470 chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- 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 = 0.4256 r_free = 0.4256 target = 0.145466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.120410 restraints weight = 15534.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.122635 restraints weight = 13012.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.124663 restraints weight = 11204.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.126296 restraints weight = 9751.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.127681 restraints weight = 8642.746| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6347 moved from start: 0.8272 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= 0.142 Angle : 0.792 9.333 5222 Z= 0.391 Chirality : 0.045 0.149 575 Planarity : 0.004 0.049 660 Dihedral : 4.951 19.379 505 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.39), residues: 445 helix: 0.99 (0.25), residues: 381 sheet: None (None), residues: 0 loop : -4.47 (0.60), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 549 TYR 0.023 0.002 TYR A 576 PHE 0.037 0.002 PHE A 13 TRP 0.017 0.002 TRP A 149 HIS 0.015 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 3881) covalent geometry : angle 0.79196 ( 5222) hydrogen bonds : bond 0.04165 ( 309) hydrogen bonds : angle 4.56665 ( 927) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 864.97 seconds wall clock time: 15 minutes 33.31 seconds (933.31 seconds total)