Starting phenix.real_space_refine on Sat Apr 4 20:48:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jbs_61324/04_2026/9jbs_61324_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jbs_61324/04_2026/9jbs_61324.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jbs_61324/04_2026/9jbs_61324_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jbs_61324/04_2026/9jbs_61324_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jbs_61324/04_2026/9jbs_61324.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jbs_61324/04_2026/9jbs_61324.map" } resolution = 2.88 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= -0.001 sd= 0.043 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 30 5.16 5 C 2129 2.51 5 N 511 2.21 5 O 537 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 3207 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3207 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 15, 'TRANS': 399} Chain breaks: 3 Time building chain proxies: 0.73, per 1000 atoms: 0.23 Number of scatterers: 3207 At special positions: 0 Unit cell: (76.728, 50.04, 70.89, 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 30 16.00 O 537 8.00 N 511 7.00 C 2129 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 81 " 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: 0.21 Conformation dependent library (CDL) restraints added in 124.8 milliseconds 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 1 sheets defined 92.5% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 4 through 11 Processing helix chain 'A' and resid 11 through 27 Processing helix chain 'A' and resid 28 through 31 Processing helix chain 'A' and resid 32 through 43 removed outlier: 3.658A pdb=" N LEU A 36 " --> pdb=" O GLY A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 50 Processing helix chain 'A' and resid 81 through 102 Processing helix chain 'A' and resid 102 through 114 Processing helix chain 'A' and resid 114 through 139 Processing helix chain 'A' and resid 139 through 144 Processing helix chain 'A' and resid 145 through 166 removed outlier: 4.086A pdb=" N ILE A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 175 through 190 Processing helix chain 'A' and resid 192 through 203 Processing helix chain 'A' and resid 206 through 228 Processing helix chain 'A' and resid 315 through 321 Processing helix chain 'A' and resid 321 through 353 removed outlier: 5.389A pdb=" N ASN A 346 " --> pdb=" O MET A 342 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ASN A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 371 Processing helix chain 'A' and resid 372 through 386 removed outlier: 4.179A pdb=" N LEU A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Proline residue: A 379 - end of helix Processing helix chain 'A' and resid 416 through 444 Processing helix chain 'A' and resid 449 through 475 removed outlier: 4.444A pdb=" N HIS A 465 " --> pdb=" O ARG A 461 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N SER A 466 " --> pdb=" O GLY A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 479 No H-bonds generated for 'chain 'A' and resid 477 through 479' Processing helix chain 'A' and resid 480 through 497 Processing helix chain 'A' and resid 498 through 507 Processing helix chain 'A' and resid 508 through 511 Processing helix chain 'A' and resid 514 through 526 removed outlier: 3.602A pdb=" N LEU A 526 " --> pdb=" O LEU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 545 Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 75 removed outlier: 4.137A pdb=" N SER A 73 " --> pdb=" O SER A 80 " (cutoff:3.500A) 277 hydrogen bonds defined for protein. 807 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: 0.54 Time building geometry restraints manager: 0.30 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: 958 1.34 - 1.46: 793 1.46 - 1.58: 1484 1.58 - 1.69: 0 1.69 - 1.81: 47 Bond restraints: 3282 Sorted by residual: bond pdb=" CA SER A 190 " pdb=" CB SER A 190 " ideal model delta sigma weight residual 1.530 1.451 0.079 1.87e-02 2.86e+03 1.79e+01 bond pdb=" N SER A 189 " pdb=" CA SER A 189 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.32e-02 5.74e+03 5.25e+00 bond pdb=" N SER A 190 " pdb=" CA SER A 190 " ideal model delta sigma weight residual 1.457 1.486 -0.028 1.35e-02 5.49e+03 4.43e+00 bond pdb=" CA ALA A 191 " pdb=" CB ALA A 191 " ideal model delta sigma weight residual 1.530 1.494 0.036 1.87e-02 2.86e+03 3.73e+00 bond pdb=" CA SER A 189 " pdb=" CB SER A 189 " ideal model delta sigma weight residual 1.532 1.507 0.025 1.78e-02 3.16e+03 2.00e+00 ... (remaining 3277 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.92: 4286 0.92 - 1.84: 144 1.84 - 2.76: 16 2.76 - 3.68: 8 3.68 - 4.60: 6 Bond angle restraints: 4460 Sorted by residual: angle pdb=" N ALA A 191 " pdb=" CA ALA A 191 " pdb=" C ALA A 191 " ideal model delta sigma weight residual 112.87 108.84 4.03 1.20e+00 6.94e-01 1.13e+01 angle pdb=" N SER A 190 " pdb=" CA SER A 190 " pdb=" C SER A 190 " ideal model delta sigma weight residual 112.87 110.08 2.79 1.20e+00 6.94e-01 5.39e+00 angle pdb=" N VAL A 353 " pdb=" CA VAL A 353 " pdb=" C VAL A 353 " ideal model delta sigma weight residual 111.91 110.31 1.60 8.90e-01 1.26e+00 3.22e+00 angle pdb=" CA SER A 189 " pdb=" C SER A 189 " pdb=" O SER A 189 " ideal model delta sigma weight residual 119.28 117.18 2.10 1.21e+00 6.83e-01 3.00e+00 angle pdb=" C VAL A 353 " pdb=" CA VAL A 353 " pdb=" CB VAL A 353 " ideal model delta sigma weight residual 112.19 110.65 1.54 1.15e+00 7.56e-01 1.79e+00 ... (remaining 4455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.28: 1820 16.28 - 32.55: 68 32.55 - 48.83: 10 48.83 - 65.11: 5 65.11 - 81.38: 1 Dihedral angle restraints: 1904 sinusoidal: 718 harmonic: 1186 Sorted by residual: dihedral pdb=" CA PHE A 463 " pdb=" C PHE A 463 " pdb=" N ILE A 464 " pdb=" CA ILE A 464 " ideal model delta harmonic sigma weight residual -180.00 -162.57 -17.43 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA ARG A 116 " pdb=" CB ARG A 116 " pdb=" CG ARG A 116 " pdb=" CD ARG A 116 " ideal model delta sinusoidal sigma weight residual -60.00 -116.29 56.29 3 1.50e+01 4.44e-03 9.39e+00 dihedral pdb=" N GLN A 419 " pdb=" CA GLN A 419 " pdb=" CB GLN A 419 " pdb=" CG GLN A 419 " ideal model delta sinusoidal sigma weight residual -180.00 -126.46 -53.54 3 1.50e+01 4.44e-03 9.21e+00 ... (remaining 1901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 332 0.022 - 0.043: 114 0.043 - 0.065: 44 0.065 - 0.087: 35 0.087 - 0.108: 10 Chirality restraints: 535 Sorted by residual: chirality pdb=" CA ILE A 444 " pdb=" N ILE A 444 " pdb=" C ILE A 444 " pdb=" CB ILE A 444 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.93e-01 chirality pdb=" CA PRO A 169 " pdb=" N PRO A 169 " pdb=" C PRO A 169 " pdb=" CB PRO A 169 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.47e-01 chirality pdb=" CA ILE A 536 " pdb=" N ILE A 536 " pdb=" C ILE A 536 " pdb=" CB ILE A 536 " both_signs ideal model delta sigma weight residual False 2.43 2.53 -0.10 2.00e-01 2.50e+01 2.35e-01 ... (remaining 532 not shown) Planarity restraints: 537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 194 " -0.037 5.00e-02 4.00e+02 5.69e-02 5.17e+00 pdb=" N PRO A 195 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 195 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 195 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 531 " 0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO A 532 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 532 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 532 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 500 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO A 501 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 501 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 501 " 0.020 5.00e-02 4.00e+02 ... (remaining 534 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 453 2.75 - 3.29: 3579 3.29 - 3.82: 5990 3.82 - 4.36: 7044 4.36 - 4.90: 11861 Nonbonded interactions: 28927 Sorted by model distance: nonbonded pdb=" OD1 ASN A 224 " pdb=" ND2 ASN A 228 " model vdw 2.210 3.120 nonbonded pdb=" OE1 GLN A 371 " pdb=" NH1 ARG A 461 " model vdw 2.230 3.120 nonbonded pdb=" O ASN A 23 " pdb=" OG SER A 27 " model vdw 2.264 3.040 nonbonded pdb=" OG SER A 42 " pdb=" OH TYR A 201 " model vdw 2.273 3.040 nonbonded pdb=" O ALA A 188 " pdb=" NH2 ARG A 461 " model vdw 2.275 3.120 ... (remaining 28922 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: 2.550 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 4.800 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:8.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 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 : 0.003 0.079 3283 Z= 0.150 Angle : 0.427 4.603 4462 Z= 0.242 Chirality : 0.032 0.108 535 Planarity : 0.004 0.057 537 Dihedral : 9.742 81.382 1139 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.71 % Allowed : 1.14 % Favored : 97.14 % 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: 2.95 (0.42), residues: 407 helix: 2.22 (0.27), residues: 343 sheet: None (None), residues: 0 loop : 0.58 (0.88), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 461 TYR 0.009 0.001 TYR A 534 PHE 0.008 0.001 PHE A 207 TRP 0.007 0.001 TRP A 33 HIS 0.002 0.000 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 3282) covalent geometry : angle 0.42681 ( 4460) SS BOND : bond 0.00106 ( 1) SS BOND : angle 0.39370 ( 2) hydrogen bonds : bond 0.09794 ( 277) hydrogen bonds : angle 4.99712 ( 807) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.091 Fit side-chains revert: symmetry clash REVERT: A 198 LYS cc_start: 0.7800 (tttm) cc_final: 0.7452 (ttpt) REVERT: A 345 MET cc_start: 0.7847 (ttm) cc_final: 0.7546 (mtp) outliers start: 6 outliers final: 0 residues processed: 88 average time/residue: 0.4779 time to fit residues: 43.2855 Evaluate side-chains 56 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.147433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.129843 restraints weight = 3459.601| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.08 r_work: 0.3349 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3283 Z= 0.171 Angle : 0.580 6.171 4462 Z= 0.299 Chirality : 0.041 0.141 535 Planarity : 0.005 0.060 537 Dihedral : 4.080 21.205 438 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.43 % Allowed : 10.00 % Favored : 86.57 % 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: 2.93 (0.42), residues: 407 helix: 2.02 (0.27), residues: 353 sheet: None (None), residues: 0 loop : 1.68 (1.16), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 119 TYR 0.008 0.001 TYR A 476 PHE 0.011 0.002 PHE A 26 TRP 0.010 0.001 TRP A 74 HIS 0.004 0.001 HIS A 465 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 3282) covalent geometry : angle 0.57984 ( 4460) SS BOND : bond 0.00126 ( 1) SS BOND : angle 0.37249 ( 2) hydrogen bonds : bond 0.04061 ( 277) hydrogen bonds : angle 4.12494 ( 807) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.115 Fit side-chains REVERT: A 345 MET cc_start: 0.8245 (ttm) cc_final: 0.7568 (mtm) outliers start: 12 outliers final: 4 residues processed: 73 average time/residue: 0.4060 time to fit residues: 30.6980 Evaluate side-chains 60 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 433 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 GLN A 432 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.144819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.126836 restraints weight = 3431.859| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.08 r_work: 0.3307 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3283 Z= 0.194 Angle : 0.599 6.792 4462 Z= 0.304 Chirality : 0.041 0.122 535 Planarity : 0.005 0.060 537 Dihedral : 4.206 22.476 438 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.43 % Allowed : 12.57 % Favored : 84.00 % 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: 2.65 (0.42), residues: 407 helix: 1.83 (0.27), residues: 353 sheet: None (None), residues: 0 loop : 1.63 (1.15), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 119 TYR 0.011 0.002 TYR A 534 PHE 0.011 0.002 PHE A 163 TRP 0.010 0.001 TRP A 33 HIS 0.003 0.001 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 3282) covalent geometry : angle 0.59870 ( 4460) SS BOND : bond 0.00194 ( 1) SS BOND : angle 0.59709 ( 2) hydrogen bonds : bond 0.04228 ( 277) hydrogen bonds : angle 4.22828 ( 807) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.142 Fit side-chains REVERT: A 11 ARG cc_start: 0.7416 (ttp-170) cc_final: 0.6877 (ttt180) outliers start: 12 outliers final: 5 residues processed: 64 average time/residue: 0.4587 time to fit residues: 30.3306 Evaluate side-chains 60 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 527 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 432 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.143414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.124457 restraints weight = 3427.731| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.19 r_work: 0.3293 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3283 Z= 0.193 Angle : 0.590 7.324 4462 Z= 0.301 Chirality : 0.041 0.121 535 Planarity : 0.005 0.059 537 Dihedral : 4.253 22.643 438 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.14 % Allowed : 12.29 % Favored : 84.57 % 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: 2.46 (0.42), residues: 407 helix: 1.72 (0.27), residues: 352 sheet: None (None), residues: 0 loop : 1.43 (1.09), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 119 TYR 0.013 0.002 TYR A 534 PHE 0.010 0.002 PHE A 163 TRP 0.010 0.001 TRP A 33 HIS 0.003 0.001 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 3282) covalent geometry : angle 0.58963 ( 4460) SS BOND : bond 0.00188 ( 1) SS BOND : angle 0.56554 ( 2) hydrogen bonds : bond 0.04220 ( 277) hydrogen bonds : angle 4.27466 ( 807) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.110 Fit side-chains REVERT: A 11 ARG cc_start: 0.7364 (ttp-170) cc_final: 0.6874 (ttt180) REVERT: A 166 LEU cc_start: 0.8487 (mm) cc_final: 0.8152 (mt) REVERT: A 420 LYS cc_start: 0.6388 (OUTLIER) cc_final: 0.6068 (mttp) outliers start: 11 outliers final: 5 residues processed: 64 average time/residue: 0.4981 time to fit residues: 32.8552 Evaluate side-chains 61 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 527 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 17 optimal weight: 0.0370 chunk 20 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 GLN A 432 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.144937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.126272 restraints weight = 3433.153| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.18 r_work: 0.3307 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3283 Z= 0.162 Angle : 0.567 7.067 4462 Z= 0.291 Chirality : 0.039 0.122 535 Planarity : 0.005 0.059 537 Dihedral : 4.184 22.611 438 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.43 % Allowed : 12.57 % Favored : 84.00 % 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: 2.54 (0.42), residues: 407 helix: 1.78 (0.27), residues: 352 sheet: None (None), residues: 0 loop : 1.45 (1.11), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 540 TYR 0.011 0.001 TYR A 534 PHE 0.012 0.002 PHE A 463 TRP 0.010 0.001 TRP A 33 HIS 0.003 0.001 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 3282) covalent geometry : angle 0.56746 ( 4460) SS BOND : bond 0.00163 ( 1) SS BOND : angle 0.55340 ( 2) hydrogen bonds : bond 0.03964 ( 277) hydrogen bonds : angle 4.20843 ( 807) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.120 Fit side-chains REVERT: A 11 ARG cc_start: 0.7433 (ttp-170) cc_final: 0.6912 (ttt180) REVERT: A 166 LEU cc_start: 0.8330 (mm) cc_final: 0.8010 (mt) REVERT: A 420 LYS cc_start: 0.6291 (OUTLIER) cc_final: 0.5867 (mttp) outliers start: 12 outliers final: 3 residues processed: 72 average time/residue: 0.4936 time to fit residues: 36.6577 Evaluate side-chains 66 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 527 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 34 optimal weight: 0.0370 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 432 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.144886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.125872 restraints weight = 3411.332| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.20 r_work: 0.3310 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3283 Z= 0.172 Angle : 0.581 7.301 4462 Z= 0.297 Chirality : 0.040 0.122 535 Planarity : 0.005 0.061 537 Dihedral : 4.230 23.167 438 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.57 % Allowed : 12.86 % Favored : 82.57 % 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: 2.55 (0.42), residues: 407 helix: 1.79 (0.27), residues: 346 sheet: None (None), residues: 0 loop : 1.49 (1.01), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 540 TYR 0.013 0.001 TYR A 534 PHE 0.014 0.002 PHE A 463 TRP 0.010 0.001 TRP A 33 HIS 0.003 0.001 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 3282) covalent geometry : angle 0.58091 ( 4460) SS BOND : bond 0.00153 ( 1) SS BOND : angle 0.46895 ( 2) hydrogen bonds : bond 0.04034 ( 277) hydrogen bonds : angle 4.23957 ( 807) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.075 Fit side-chains REVERT: A 11 ARG cc_start: 0.7437 (ttp-170) cc_final: 0.6950 (ttt180) REVERT: A 166 LEU cc_start: 0.8382 (mm) cc_final: 0.8067 (mt) REVERT: A 388 ARG cc_start: 0.7373 (mtp180) cc_final: 0.7025 (mtm110) REVERT: A 420 LYS cc_start: 0.6347 (OUTLIER) cc_final: 0.5946 (mttp) outliers start: 16 outliers final: 5 residues processed: 71 average time/residue: 0.5256 time to fit residues: 38.3819 Evaluate side-chains 65 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 527 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 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 417 GLN A 432 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.145123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.126582 restraints weight = 3440.267| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.10 r_work: 0.3306 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3283 Z= 0.186 Angle : 0.614 7.835 4462 Z= 0.312 Chirality : 0.041 0.154 535 Planarity : 0.005 0.063 537 Dihedral : 4.273 23.351 438 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.00 % Allowed : 14.29 % Favored : 81.71 % 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: 2.48 (0.42), residues: 407 helix: 1.75 (0.27), residues: 346 sheet: None (None), residues: 0 loop : 1.40 (0.99), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 540 TYR 0.015 0.001 TYR A 534 PHE 0.015 0.002 PHE A 463 TRP 0.011 0.001 TRP A 13 HIS 0.003 0.001 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 3282) covalent geometry : angle 0.61381 ( 4460) SS BOND : bond 0.00168 ( 1) SS BOND : angle 0.42018 ( 2) hydrogen bonds : bond 0.04124 ( 277) hydrogen bonds : angle 4.29967 ( 807) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.136 Fit side-chains REVERT: A 11 ARG cc_start: 0.7457 (ttp-170) cc_final: 0.7023 (ttt180) REVERT: A 166 LEU cc_start: 0.8497 (mm) cc_final: 0.8175 (mt) REVERT: A 187 TYR cc_start: 0.8055 (OUTLIER) cc_final: 0.7623 (t80) REVERT: A 388 ARG cc_start: 0.7296 (mtp180) cc_final: 0.6998 (mtm110) REVERT: A 420 LYS cc_start: 0.6427 (OUTLIER) cc_final: 0.5989 (mttp) outliers start: 14 outliers final: 6 residues processed: 70 average time/residue: 0.5840 time to fit residues: 41.9945 Evaluate side-chains 68 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 527 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 20 optimal weight: 0.3980 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.147127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.129275 restraints weight = 3452.784| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.08 r_work: 0.3327 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3283 Z= 0.179 Angle : 0.608 8.814 4462 Z= 0.310 Chirality : 0.041 0.187 535 Planarity : 0.005 0.064 537 Dihedral : 4.272 23.555 438 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.43 % Allowed : 15.43 % Favored : 81.14 % 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: 2.47 (0.42), residues: 407 helix: 1.74 (0.27), residues: 346 sheet: None (None), residues: 0 loop : 1.39 (0.99), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 540 TYR 0.014 0.001 TYR A 534 PHE 0.016 0.002 PHE A 463 TRP 0.009 0.001 TRP A 33 HIS 0.003 0.001 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 3282) covalent geometry : angle 0.60793 ( 4460) SS BOND : bond 0.00156 ( 1) SS BOND : angle 0.44786 ( 2) hydrogen bonds : bond 0.04100 ( 277) hydrogen bonds : angle 4.32499 ( 807) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.117 Fit side-chains REVERT: A 11 ARG cc_start: 0.7397 (ttp-170) cc_final: 0.6958 (ttt180) REVERT: A 166 LEU cc_start: 0.8482 (mm) cc_final: 0.8156 (mt) REVERT: A 187 TYR cc_start: 0.7986 (OUTLIER) cc_final: 0.7523 (t80) REVERT: A 388 ARG cc_start: 0.7237 (mtp180) cc_final: 0.6969 (mtm110) REVERT: A 420 LYS cc_start: 0.6471 (OUTLIER) cc_final: 0.6037 (mttp) outliers start: 12 outliers final: 4 residues processed: 71 average time/residue: 0.4759 time to fit residues: 34.7768 Evaluate side-chains 67 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 527 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 chunk 20 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 GLN A 432 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.148516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.130652 restraints weight = 3450.460| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.09 r_work: 0.3346 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3283 Z= 0.156 Angle : 0.601 9.611 4462 Z= 0.307 Chirality : 0.041 0.211 535 Planarity : 0.006 0.065 537 Dihedral : 4.186 23.478 438 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.14 % Allowed : 15.14 % Favored : 81.71 % 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: 2.62 (0.42), residues: 407 helix: 1.84 (0.27), residues: 346 sheet: None (None), residues: 0 loop : 1.48 (1.01), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 116 TYR 0.014 0.001 TYR A 383 PHE 0.018 0.002 PHE A 463 TRP 0.011 0.001 TRP A 33 HIS 0.003 0.001 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 3282) covalent geometry : angle 0.60125 ( 4460) SS BOND : bond 0.00153 ( 1) SS BOND : angle 0.43631 ( 2) hydrogen bonds : bond 0.03958 ( 277) hydrogen bonds : angle 4.29778 ( 807) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.137 Fit side-chains REVERT: A 11 ARG cc_start: 0.7456 (ttp-170) cc_final: 0.6986 (ttt180) REVERT: A 166 LEU cc_start: 0.8412 (mm) cc_final: 0.8092 (mt) REVERT: A 187 TYR cc_start: 0.7964 (OUTLIER) cc_final: 0.7520 (t80) REVERT: A 388 ARG cc_start: 0.7257 (mtp180) cc_final: 0.6998 (mtm110) REVERT: A 420 LYS cc_start: 0.6438 (OUTLIER) cc_final: 0.5874 (mttp) outliers start: 11 outliers final: 4 residues processed: 70 average time/residue: 0.5301 time to fit residues: 38.1535 Evaluate side-chains 65 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 527 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 432 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.143901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.124640 restraints weight = 3403.601| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.20 r_work: 0.3288 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 3283 Z= 0.218 Angle : 0.663 10.553 4462 Z= 0.339 Chirality : 0.044 0.212 535 Planarity : 0.006 0.065 537 Dihedral : 4.361 24.092 438 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.29 % Allowed : 15.71 % Favored : 82.00 % 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 (0.42), residues: 407 helix: 1.62 (0.27), residues: 346 sheet: None (None), residues: 0 loop : 1.31 (0.97), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 540 TYR 0.017 0.002 TYR A 534 PHE 0.021 0.002 PHE A 463 TRP 0.014 0.002 TRP A 13 HIS 0.004 0.001 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00532 ( 3282) covalent geometry : angle 0.66337 ( 4460) SS BOND : bond 0.00185 ( 1) SS BOND : angle 0.43967 ( 2) hydrogen bonds : bond 0.04381 ( 277) hydrogen bonds : angle 4.50240 ( 807) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.114 Fit side-chains REVERT: A 11 ARG cc_start: 0.7442 (ttp-170) cc_final: 0.6909 (ttt180) REVERT: A 166 LEU cc_start: 0.8409 (mm) cc_final: 0.8071 (mt) REVERT: A 187 TYR cc_start: 0.8068 (OUTLIER) cc_final: 0.7575 (t80) REVERT: A 388 ARG cc_start: 0.7287 (mtp180) cc_final: 0.7007 (mtm110) REVERT: A 420 LYS cc_start: 0.6385 (OUTLIER) cc_final: 0.5990 (mttp) outliers start: 8 outliers final: 4 residues processed: 69 average time/residue: 0.5480 time to fit residues: 38.8955 Evaluate side-chains 66 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 527 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 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 432 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.143602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.124708 restraints weight = 3485.143| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.23 r_work: 0.3282 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 3283 Z= 0.192 Angle : 0.646 10.319 4462 Z= 0.331 Chirality : 0.043 0.216 535 Planarity : 0.006 0.066 537 Dihedral : 4.309 24.331 438 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.57 % Allowed : 16.00 % Favored : 81.43 % 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 (0.42), residues: 407 helix: 1.62 (0.27), residues: 346 sheet: None (None), residues: 0 loop : 1.35 (0.98), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 116 TYR 0.017 0.002 TYR A 383 PHE 0.021 0.002 PHE A 463 TRP 0.013 0.001 TRP A 13 HIS 0.003 0.001 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 3282) covalent geometry : angle 0.64648 ( 4460) SS BOND : bond 0.00182 ( 1) SS BOND : angle 0.46325 ( 2) hydrogen bonds : bond 0.04228 ( 277) hydrogen bonds : angle 4.47619 ( 807) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1283.67 seconds wall clock time: 22 minutes 42.39 seconds (1362.39 seconds total)