Starting phenix.real_space_refine on Sat Apr 4 21:54:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wx9_66339/04_2026/9wx9_66339.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wx9_66339/04_2026/9wx9_66339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wx9_66339/04_2026/9wx9_66339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wx9_66339/04_2026/9wx9_66339.map" model { file = "/net/cci-nas-00/data/ceres_data/9wx9_66339/04_2026/9wx9_66339.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wx9_66339/04_2026/9wx9_66339.cif" } resolution = 2.84 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= -0.004 sd= 0.147 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: 6 Type Number sf(0) Gaussians S 34 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 2857 2.51 5 N 657 2.21 5 O 715 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4265 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4263 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 26, 'TRANS': 513} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 0.92, per 1000 atoms: 0.22 Number of scatterers: 4265 At special positions: 0 Unit cell: (81.092, 68.288, 81.092, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 34 16.00 Na 1 11.00 O 715 8.00 N 657 7.00 C 2857 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 166 " distance=2.03 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: 0.36 Conformation dependent library (CDL) restraints added in 255.9 milliseconds 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 982 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 1 sheets defined 79.6% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 40 through 52 removed outlier: 3.536A pdb=" N LEU A 44 " --> pdb=" O TRP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 removed outlier: 3.502A pdb=" N ASN A 59 " --> pdb=" O GLY A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 69 Processing helix chain 'A' and resid 72 through 86 Proline residue: A 78 - end of helix Processing helix chain 'A' and resid 86 through 102 removed outlier: 3.547A pdb=" N LEU A 90 " --> pdb=" O CYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.599A pdb=" N TRP A 109 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 115 through 147 removed outlier: 3.993A pdb=" N GLY A 119 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET A 135 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 156 removed outlier: 4.232A pdb=" N HIS A 156 " --> pdb=" O PRO A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 214 through 234 Processing helix chain 'A' and resid 247 through 264 removed outlier: 3.515A pdb=" N THR A 263 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 276 removed outlier: 4.042A pdb=" N GLY A 270 " --> pdb=" O GLY A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.791A pdb=" N LEU A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 300 removed outlier: 4.242A pdb=" N TRP A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 311 Processing helix chain 'A' and resid 318 through 353 Processing helix chain 'A' and resid 365 through 376 Proline residue: A 372 - end of helix Processing helix chain 'A' and resid 380 through 415 removed outlier: 3.564A pdb=" N TRP A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 422 through 439 Processing helix chain 'A' and resid 440 through 443 removed outlier: 3.791A pdb=" N THR A 443 " --> pdb=" O ILE A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 440 through 443' Processing helix chain 'A' and resid 445 through 457 removed outlier: 3.656A pdb=" N TRP A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 475 Processing helix chain 'A' and resid 478 through 491 Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 504 through 520 Processing helix chain 'A' and resid 532 through 561 removed outlier: 3.839A pdb=" N SER A 546 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) Proline residue: A 551 - end of helix Processing helix chain 'A' and resid 564 through 574 Processing helix chain 'A' and resid 588 through 592 removed outlier: 3.514A pdb=" N TYR A 591 " --> pdb=" O THR A 588 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A 592 " --> pdb=" O GLY A 589 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 588 through 592' Processing sheet with id=AA1, first strand: chain 'A' and resid 525 through 526 288 hydrogen bonds defined for protein. 843 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: 0.57 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1242 1.34 - 1.46: 1015 1.46 - 1.58: 2085 1.58 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 4396 Sorted by residual: bond pdb=" N GLN A 522 " pdb=" CA GLN A 522 " ideal model delta sigma weight residual 1.462 1.498 -0.035 1.05e-02 9.07e+03 1.14e+01 bond pdb=" N ILE A 325 " pdb=" CA ILE A 325 " ideal model delta sigma weight residual 1.461 1.501 -0.040 1.19e-02 7.06e+03 1.14e+01 bond pdb=" N PHE A 249 " pdb=" CA PHE A 249 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.20e-03 1.18e+04 9.78e+00 bond pdb=" N TYR A 371 " pdb=" CA TYR A 371 " ideal model delta sigma weight residual 1.461 1.488 -0.027 9.20e-03 1.18e+04 8.83e+00 bond pdb=" N VAL A 344 " pdb=" CA VAL A 344 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.81e+00 ... (remaining 4391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 5513 1.52 - 3.05: 378 3.05 - 4.57: 80 4.57 - 6.10: 19 6.10 - 7.62: 3 Bond angle restraints: 5993 Sorted by residual: angle pdb=" N GLY A 240 " pdb=" CA GLY A 240 " pdb=" C GLY A 240 " ideal model delta sigma weight residual 115.30 108.25 7.05 1.44e+00 4.82e-01 2.40e+01 angle pdb=" N LYS A 361 " pdb=" CA LYS A 361 " pdb=" C LYS A 361 " ideal model delta sigma weight residual 113.18 107.93 5.25 1.21e+00 6.83e-01 1.89e+01 angle pdb=" CA SER A 298 " pdb=" C SER A 298 " pdb=" O SER A 298 " ideal model delta sigma weight residual 120.82 116.57 4.25 1.05e+00 9.07e-01 1.64e+01 angle pdb=" N VAL A 243 " pdb=" CA VAL A 243 " pdb=" C VAL A 243 " ideal model delta sigma weight residual 112.83 108.89 3.94 9.90e-01 1.02e+00 1.58e+01 angle pdb=" CA GLY A 396 " pdb=" C GLY A 396 " pdb=" O GLY A 396 " ideal model delta sigma weight residual 120.66 116.76 3.90 1.06e+00 8.90e-01 1.36e+01 ... (remaining 5988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.38: 2107 14.38 - 28.75: 251 28.75 - 43.13: 99 43.13 - 57.50: 32 57.50 - 71.88: 7 Dihedral angle restraints: 2496 sinusoidal: 946 harmonic: 1550 Sorted by residual: dihedral pdb=" CA TRP A 109 " pdb=" C TRP A 109 " pdb=" N LYS A 110 " pdb=" CA LYS A 110 " ideal model delta harmonic sigma weight residual 180.00 163.71 16.29 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CG ARG A 587 " pdb=" CD ARG A 587 " pdb=" NE ARG A 587 " pdb=" CZ ARG A 587 " ideal model delta sinusoidal sigma weight residual 180.00 135.81 44.19 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CG ARG A 321 " pdb=" CD ARG A 321 " pdb=" NE ARG A 321 " pdb=" CZ ARG A 321 " ideal model delta sinusoidal sigma weight residual -180.00 -137.50 -42.50 2 1.50e+01 4.44e-03 9.74e+00 ... (remaining 2493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 531 0.056 - 0.113: 113 0.113 - 0.169: 24 0.169 - 0.226: 4 0.226 - 0.282: 2 Chirality restraints: 674 Sorted by residual: chirality pdb=" CA VAL A 242 " pdb=" N VAL A 242 " pdb=" C VAL A 242 " pdb=" CB VAL A 242 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA VAL A 243 " pdb=" N VAL A 243 " pdb=" C VAL A 243 " pdb=" CB VAL A 243 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA VAL A 476 " pdb=" N VAL A 476 " pdb=" C VAL A 476 " pdb=" CB VAL A 476 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 671 not shown) Planarity restraints: 726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 236 " 0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C VAL A 236 " -0.059 2.00e-02 2.50e+03 pdb=" O VAL A 236 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS A 237 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 522 " 0.043 5.00e-02 4.00e+02 6.46e-02 6.67e+00 pdb=" N PRO A 523 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 523 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 523 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 471 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.61e+00 pdb=" C LEU A 471 " 0.044 2.00e-02 2.50e+03 pdb=" O LEU A 471 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA A 472 " -0.015 2.00e-02 2.50e+03 ... (remaining 723 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 437 2.75 - 3.29: 4407 3.29 - 3.82: 7631 3.82 - 4.36: 9467 4.36 - 4.90: 15643 Nonbonded interactions: 37585 Sorted by model distance: nonbonded pdb=" OG SER A 147 " pdb=" OG SER A 385 " model vdw 2.210 3.040 nonbonded pdb=" O ALA A 84 " pdb=" OH TYR A 497 " model vdw 2.254 3.040 nonbonded pdb=" OG SER A 298 " pdb="NA NA A 701 " model vdw 2.355 2.470 nonbonded pdb=" O LEU A 378 " pdb=" OG SER A 381 " model vdw 2.359 3.040 nonbonded pdb=" OH TYR A 456 " pdb=" OE1 GLU A 536 " model vdw 2.382 3.040 ... (remaining 37580 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 individual isotropic 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: 1.220 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.470 Find NCS groups from input model: 0.010 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:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5903 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 : 0.006 0.057 4397 Z= 0.398 Angle : 0.869 7.622 5995 Z= 0.593 Chirality : 0.052 0.282 674 Planarity : 0.006 0.065 726 Dihedral : 15.596 71.880 1511 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 18.98 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 (0.36), residues: 536 helix: 0.84 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -1.57 (0.45), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 420 TYR 0.016 0.002 TYR A 132 PHE 0.015 0.001 PHE A 309 TRP 0.027 0.002 TRP A 215 HIS 0.006 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00572 ( 4396) covalent geometry : angle 0.86863 ( 5993) SS BOND : bond 0.00332 ( 1) SS BOND : angle 0.60315 ( 2) hydrogen bonds : bond 0.12510 ( 288) hydrogen bonds : angle 6.13938 ( 843) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.106 Fit side-chains REVERT: A 94 GLU cc_start: 0.6849 (tt0) cc_final: 0.6647 (tt0) REVERT: A 289 ILE cc_start: 0.6519 (mt) cc_final: 0.6144 (mt) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.3728 time to fit residues: 38.3618 Evaluate side-chains 71 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.0870 chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.163904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.141513 restraints weight = 4773.911| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.38 r_work: 0.3378 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 4397 Z= 0.307 Angle : 0.758 7.557 5995 Z= 0.395 Chirality : 0.046 0.309 674 Planarity : 0.006 0.044 726 Dihedral : 4.461 22.203 584 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.86 % Allowed : 17.44 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.91 (0.35), residues: 536 helix: 1.36 (0.26), residues: 373 sheet: None (None), residues: 0 loop : -1.14 (0.47), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 587 TYR 0.022 0.002 TYR A 143 PHE 0.026 0.002 PHE A 91 TRP 0.029 0.003 TRP A 534 HIS 0.012 0.002 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00517 ( 4396) covalent geometry : angle 0.75795 ( 5993) SS BOND : bond 0.00039 ( 1) SS BOND : angle 1.69037 ( 2) hydrogen bonds : bond 0.05117 ( 288) hydrogen bonds : angle 4.79561 ( 843) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.8333 (mt) cc_final: 0.8113 (mm) REVERT: A 135 MET cc_start: 0.8966 (tpt) cc_final: 0.8269 (tpt) REVERT: A 212 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.6343 (pp20) REVERT: A 230 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7666 (mt) REVERT: A 284 SER cc_start: 0.7761 (OUTLIER) cc_final: 0.7460 (p) REVERT: A 332 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7538 (mt) REVERT: A 358 GLN cc_start: 0.7202 (pt0) cc_final: 0.6982 (pt0) REVERT: A 585 GLU cc_start: 0.7397 (mp0) cc_final: 0.7181 (pm20) outliers start: 22 outliers final: 4 residues processed: 97 average time/residue: 0.4021 time to fit residues: 40.7865 Evaluate side-chains 74 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 483 CYS Chi-restraints excluded: chain A residue 590 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 43 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 8 optimal weight: 0.2980 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 30 optimal weight: 0.0060 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.145408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.121682 restraints weight = 4647.443| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.40 r_work: 0.3137 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.6554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4397 Z= 0.180 Angle : 0.638 7.715 5995 Z= 0.323 Chirality : 0.042 0.206 674 Planarity : 0.005 0.048 726 Dihedral : 4.124 19.258 584 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.42 % Allowed : 20.75 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.54 (0.36), residues: 536 helix: 1.78 (0.26), residues: 372 sheet: None (None), residues: 0 loop : -0.73 (0.48), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 587 TYR 0.016 0.002 TYR A 132 PHE 0.016 0.001 PHE A 91 TRP 0.024 0.002 TRP A 534 HIS 0.012 0.002 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 4396) covalent geometry : angle 0.63065 ( 5993) SS BOND : bond 0.00695 ( 1) SS BOND : angle 5.14970 ( 2) hydrogen bonds : bond 0.04908 ( 288) hydrogen bonds : angle 4.51795 ( 843) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.163 Fit side-chains REVERT: A 85 ILE cc_start: 0.8150 (mt) cc_final: 0.7939 (mp) REVERT: A 212 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7849 (mm-30) REVERT: A 230 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7795 (mt) REVERT: A 332 ILE cc_start: 0.8484 (mp) cc_final: 0.8209 (mt) REVERT: A 358 GLN cc_start: 0.7696 (pt0) cc_final: 0.7367 (pt0) REVERT: A 375 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7358 (mpp) REVERT: A 434 MET cc_start: 0.8310 (mtt) cc_final: 0.7891 (mtt) REVERT: A 468 THR cc_start: 0.8215 (m) cc_final: 0.7960 (m) REVERT: A 514 MET cc_start: 0.7171 (mpp) cc_final: 0.6822 (mtt) outliers start: 20 outliers final: 6 residues processed: 85 average time/residue: 0.4340 time to fit residues: 38.5953 Evaluate side-chains 73 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 590 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS A 522 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.131764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.107113 restraints weight = 4651.931| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.45 r_work: 0.2973 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.8198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 4397 Z= 0.173 Angle : 0.600 5.824 5995 Z= 0.302 Chirality : 0.042 0.184 674 Planarity : 0.005 0.042 726 Dihedral : 4.160 19.984 584 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 5.52 % Allowed : 20.53 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.65 (0.36), residues: 536 helix: 1.81 (0.26), residues: 372 sheet: None (None), residues: 0 loop : -0.54 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 568 TYR 0.018 0.002 TYR A 132 PHE 0.012 0.002 PHE A 75 TRP 0.016 0.002 TRP A 534 HIS 0.002 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 4396) covalent geometry : angle 0.59858 ( 5993) SS BOND : bond 0.00097 ( 1) SS BOND : angle 2.16819 ( 2) hydrogen bonds : bond 0.04971 ( 288) hydrogen bonds : angle 4.55348 ( 843) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.148 Fit side-chains REVERT: A 212 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7913 (mm-30) REVERT: A 332 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8135 (mt) REVERT: A 358 GLN cc_start: 0.8065 (pt0) cc_final: 0.7640 (pt0) REVERT: A 434 MET cc_start: 0.8373 (mtt) cc_final: 0.7994 (mtt) REVERT: A 570 GLN cc_start: 0.6294 (tp40) cc_final: 0.5869 (mt0) outliers start: 25 outliers final: 7 residues processed: 92 average time/residue: 0.4612 time to fit residues: 44.2957 Evaluate side-chains 83 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 590 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 2 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 42 optimal weight: 0.0870 chunk 52 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.3381 r_free = 0.3381 target = 0.129883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.105965 restraints weight = 4690.905| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.44 r_work: 0.2948 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.8843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4397 Z= 0.146 Angle : 0.542 6.650 5995 Z= 0.274 Chirality : 0.040 0.208 674 Planarity : 0.004 0.036 726 Dihedral : 4.036 19.066 584 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 4.86 % Allowed : 20.09 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.10 (0.36), residues: 536 helix: 2.08 (0.26), residues: 373 sheet: None (None), residues: 0 loop : -0.19 (0.51), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 568 TYR 0.020 0.002 TYR A 320 PHE 0.011 0.001 PHE A 389 TRP 0.015 0.001 TRP A 534 HIS 0.003 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 4396) covalent geometry : angle 0.54091 ( 5993) SS BOND : bond 0.00387 ( 1) SS BOND : angle 2.00227 ( 2) hydrogen bonds : bond 0.04657 ( 288) hydrogen bonds : angle 4.49070 ( 843) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.112 Fit side-chains REVERT: A 81 LEU cc_start: 0.8410 (mt) cc_final: 0.8161 (mt) REVERT: A 82 MET cc_start: 0.8961 (mmm) cc_final: 0.8643 (mmm) REVERT: A 212 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7905 (mm-30) REVERT: A 332 ILE cc_start: 0.8491 (mp) cc_final: 0.8114 (mt) REVERT: A 380 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8168 (mp) REVERT: A 434 MET cc_start: 0.8315 (mtt) cc_final: 0.7984 (mtt) REVERT: A 570 GLN cc_start: 0.6506 (tp40) cc_final: 0.6172 (mt0) outliers start: 22 outliers final: 9 residues processed: 99 average time/residue: 0.4749 time to fit residues: 48.9131 Evaluate side-chains 91 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 555 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3302 r_free = 0.3302 target = 0.123632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.099643 restraints weight = 4763.951| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.48 r_work: 0.2894 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.9463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4397 Z= 0.186 Angle : 0.597 6.442 5995 Z= 0.299 Chirality : 0.043 0.238 674 Planarity : 0.004 0.036 726 Dihedral : 4.181 19.708 584 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 6.40 % Allowed : 21.19 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.00 (0.36), residues: 536 helix: 1.97 (0.26), residues: 372 sheet: None (None), residues: 0 loop : -0.14 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 530 TYR 0.021 0.002 TYR A 320 PHE 0.015 0.002 PHE A 460 TRP 0.031 0.002 TRP A 534 HIS 0.003 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 4396) covalent geometry : angle 0.59519 ( 5993) SS BOND : bond 0.00273 ( 1) SS BOND : angle 2.40521 ( 2) hydrogen bonds : bond 0.05025 ( 288) hydrogen bonds : angle 4.60946 ( 843) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 76 time to evaluate : 0.164 Fit side-chains REVERT: A 82 MET cc_start: 0.8838 (mmm) cc_final: 0.8556 (mmp) REVERT: A 167 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8118 (tp) REVERT: A 191 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8083 (tp30) REVERT: A 212 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7912 (mm-30) REVERT: A 272 GLN cc_start: 0.7823 (tt0) cc_final: 0.7358 (mt0) REVERT: A 332 ILE cc_start: 0.8476 (mp) cc_final: 0.8095 (mt) REVERT: A 351 GLU cc_start: 0.7875 (tt0) cc_final: 0.7597 (tt0) REVERT: A 380 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8414 (mp) REVERT: A 536 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7798 (mm-30) REVERT: A 537 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7705 (tm) REVERT: A 555 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7151 (tm) REVERT: A 570 GLN cc_start: 0.6891 (tp40) cc_final: 0.6686 (mt0) outliers start: 29 outliers final: 11 residues processed: 92 average time/residue: 0.5062 time to fit residues: 48.3833 Evaluate side-chains 91 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 584 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 46 optimal weight: 0.5980 chunk 31 optimal weight: 0.0980 chunk 21 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 0.0980 chunk 29 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.3580 ------------------------------------------------------------------------------- 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 = 0.3328 r_free = 0.3328 target = 0.125619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.101935 restraints weight = 4655.700| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.46 r_work: 0.2958 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.9629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4397 Z= 0.125 Angle : 0.531 7.747 5995 Z= 0.265 Chirality : 0.041 0.233 674 Planarity : 0.004 0.036 726 Dihedral : 3.965 19.228 584 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 5.30 % Allowed : 21.85 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.29 (0.36), residues: 536 helix: 2.22 (0.26), residues: 372 sheet: None (None), residues: 0 loop : -0.08 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 560 TYR 0.017 0.001 TYR A 132 PHE 0.016 0.001 PHE A 460 TRP 0.025 0.001 TRP A 534 HIS 0.001 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 4396) covalent geometry : angle 0.53040 ( 5993) SS BOND : bond 0.00260 ( 1) SS BOND : angle 1.64219 ( 2) hydrogen bonds : bond 0.04427 ( 288) hydrogen bonds : angle 4.41177 ( 843) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.154 Fit side-chains REVERT: A 82 MET cc_start: 0.8731 (mmm) cc_final: 0.8522 (mmp) REVERT: A 156 HIS cc_start: 0.7759 (m90) cc_final: 0.7442 (m-70) REVERT: A 167 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7980 (tp) REVERT: A 191 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8114 (tp30) REVERT: A 332 ILE cc_start: 0.8419 (mp) cc_final: 0.8028 (mt) REVERT: A 351 GLU cc_start: 0.7870 (tt0) cc_final: 0.7610 (tt0) REVERT: A 380 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8353 (mp) REVERT: A 480 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7670 (mp10) REVERT: A 499 ARG cc_start: 0.7763 (mtm110) cc_final: 0.7175 (mtt-85) REVERT: A 528 SER cc_start: 0.8401 (m) cc_final: 0.8106 (p) REVERT: A 536 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7949 (mm-30) REVERT: A 537 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7641 (tm) REVERT: A 555 LEU cc_start: 0.7619 (mm) cc_final: 0.7138 (tm) REVERT: A 559 LEU cc_start: 0.8418 (mm) cc_final: 0.7919 (mm) outliers start: 24 outliers final: 6 residues processed: 89 average time/residue: 0.5327 time to fit residues: 49.1293 Evaluate side-chains 88 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 537 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 12 optimal weight: 0.0050 chunk 45 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 chunk 17 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 overall best weight: 0.3994 ------------------------------------------------------------------------------- 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 = 0.3310 r_free = 0.3310 target = 0.124500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.102172 restraints weight = 4641.862| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.30 r_work: 0.2881 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.9707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4397 Z= 0.130 Angle : 0.539 7.710 5995 Z= 0.267 Chirality : 0.041 0.244 674 Planarity : 0.004 0.035 726 Dihedral : 3.925 19.395 584 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.64 % Allowed : 22.08 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.35 (0.37), residues: 536 helix: 2.26 (0.26), residues: 372 sheet: None (None), residues: 0 loop : -0.05 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 560 TYR 0.018 0.002 TYR A 132 PHE 0.023 0.001 PHE A 460 TRP 0.023 0.001 TRP A 534 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 4396) covalent geometry : angle 0.53810 ( 5993) SS BOND : bond 0.00250 ( 1) SS BOND : angle 1.71139 ( 2) hydrogen bonds : bond 0.04404 ( 288) hydrogen bonds : angle 4.40686 ( 843) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.108 Fit side-chains REVERT: A 82 MET cc_start: 0.8818 (mmm) cc_final: 0.8609 (mmp) REVERT: A 156 HIS cc_start: 0.7788 (m90) cc_final: 0.7472 (m-70) REVERT: A 167 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8006 (tp) REVERT: A 234 LYS cc_start: 0.8313 (mmmt) cc_final: 0.6813 (tmtt) REVERT: A 332 ILE cc_start: 0.8596 (mp) cc_final: 0.8220 (mt) REVERT: A 351 GLU cc_start: 0.7997 (tt0) cc_final: 0.7749 (tt0) REVERT: A 380 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8527 (mp) REVERT: A 480 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7779 (mp10) REVERT: A 499 ARG cc_start: 0.7930 (mtm110) cc_final: 0.7416 (mtt-85) REVERT: A 528 SER cc_start: 0.8234 (m) cc_final: 0.8008 (p) REVERT: A 536 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8042 (mm-30) REVERT: A 549 MET cc_start: 0.8808 (ttp) cc_final: 0.8563 (ttp) REVERT: A 555 LEU cc_start: 0.7705 (mm) cc_final: 0.7488 (tm) outliers start: 21 outliers final: 8 residues processed: 87 average time/residue: 0.5417 time to fit residues: 48.8711 Evaluate side-chains 88 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 536 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 0.0670 chunk 43 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 7 optimal weight: 0.0970 chunk 23 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.4116 ------------------------------------------------------------------------------- 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 = 0.3313 r_free = 0.3313 target = 0.124584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.102858 restraints weight = 4708.881| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.27 r_work: 0.2891 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.9824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4397 Z= 0.128 Angle : 0.542 8.372 5995 Z= 0.268 Chirality : 0.041 0.260 674 Planarity : 0.004 0.035 726 Dihedral : 3.910 19.358 584 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.75 % Allowed : 23.18 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.37 (0.36), residues: 536 helix: 2.28 (0.26), residues: 372 sheet: None (None), residues: 0 loop : -0.06 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 560 TYR 0.018 0.001 TYR A 132 PHE 0.029 0.001 PHE A 460 TRP 0.020 0.001 TRP A 534 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 4396) covalent geometry : angle 0.54168 ( 5993) SS BOND : bond 0.00258 ( 1) SS BOND : angle 1.68531 ( 2) hydrogen bonds : bond 0.04384 ( 288) hydrogen bonds : angle 4.40540 ( 843) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.167 Fit side-chains REVERT: A 82 MET cc_start: 0.8813 (mmm) cc_final: 0.8603 (mmp) REVERT: A 156 HIS cc_start: 0.7774 (m90) cc_final: 0.7466 (m-70) REVERT: A 167 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8028 (tp) REVERT: A 191 GLU cc_start: 0.9066 (OUTLIER) cc_final: 0.8134 (tp30) REVERT: A 234 LYS cc_start: 0.8282 (mmmt) cc_final: 0.6787 (tmtt) REVERT: A 332 ILE cc_start: 0.8583 (mp) cc_final: 0.8209 (mt) REVERT: A 351 GLU cc_start: 0.7994 (tt0) cc_final: 0.7760 (tt0) REVERT: A 380 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8543 (mp) REVERT: A 480 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7748 (mp10) REVERT: A 499 ARG cc_start: 0.7938 (mtm110) cc_final: 0.7463 (mtt-85) REVERT: A 528 SER cc_start: 0.8214 (m) cc_final: 0.8002 (p) REVERT: A 536 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8038 (mm-30) REVERT: A 588 THR cc_start: 0.8530 (p) cc_final: 0.8217 (t) outliers start: 17 outliers final: 7 residues processed: 86 average time/residue: 0.5730 time to fit residues: 51.0365 Evaluate side-chains 87 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 536 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 40 optimal weight: 0.4980 chunk 35 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.122329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.100424 restraints weight = 4637.295| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.29 r_work: 0.2860 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.9956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4397 Z= 0.155 Angle : 0.582 8.840 5995 Z= 0.286 Chirality : 0.042 0.290 674 Planarity : 0.004 0.036 726 Dihedral : 4.038 19.516 584 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.97 % Allowed : 22.08 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.25 (0.36), residues: 536 helix: 2.16 (0.26), residues: 372 sheet: None (None), residues: 0 loop : -0.03 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 560 TYR 0.018 0.002 TYR A 132 PHE 0.038 0.002 PHE A 460 TRP 0.020 0.002 TRP A 215 HIS 0.003 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 4396) covalent geometry : angle 0.58117 ( 5993) SS BOND : bond 0.00292 ( 1) SS BOND : angle 2.07255 ( 2) hydrogen bonds : bond 0.04685 ( 288) hydrogen bonds : angle 4.52573 ( 843) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.189 Fit side-chains REVERT: A 82 MET cc_start: 0.8854 (mmm) cc_final: 0.8628 (mmp) REVERT: A 156 HIS cc_start: 0.7865 (m90) cc_final: 0.7537 (m-70) REVERT: A 167 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8135 (tp) REVERT: A 191 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8148 (tp30) REVERT: A 234 LYS cc_start: 0.8318 (mmmt) cc_final: 0.6823 (tmtt) REVERT: A 332 ILE cc_start: 0.8586 (mp) cc_final: 0.8220 (mt) REVERT: A 351 GLU cc_start: 0.8044 (tt0) cc_final: 0.7801 (tt0) REVERT: A 460 PHE cc_start: 0.7644 (t80) cc_final: 0.7181 (p90) REVERT: A 480 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7790 (mp10) REVERT: A 499 ARG cc_start: 0.8040 (mtm110) cc_final: 0.7498 (mtt-85) REVERT: A 536 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7863 (mm-30) REVERT: A 588 THR cc_start: 0.8571 (p) cc_final: 0.8235 (t) outliers start: 18 outliers final: 7 residues processed: 82 average time/residue: 0.5772 time to fit residues: 49.0981 Evaluate side-chains 83 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 536 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 14 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3291 r_free = 0.3291 target = 0.123050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.101692 restraints weight = 4649.848| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.26 r_work: 0.2875 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.9978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4397 Z= 0.138 Angle : 0.560 8.850 5995 Z= 0.275 Chirality : 0.041 0.278 674 Planarity : 0.004 0.037 726 Dihedral : 3.971 19.326 584 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.97 % Allowed : 21.85 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.29 (0.36), residues: 536 helix: 2.19 (0.26), residues: 372 sheet: None (None), residues: 0 loop : -0.00 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 560 TYR 0.018 0.002 TYR A 132 PHE 0.037 0.001 PHE A 460 TRP 0.024 0.002 TRP A 215 HIS 0.002 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 4396) covalent geometry : angle 0.55959 ( 5993) SS BOND : bond 0.00257 ( 1) SS BOND : angle 1.81715 ( 2) hydrogen bonds : bond 0.04521 ( 288) hydrogen bonds : angle 4.46739 ( 843) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1711.05 seconds wall clock time: 29 minutes 50.80 seconds (1790.80 seconds total)