Starting phenix.real_space_refine on Wed Sep 17 04:37:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kr7_62521/09_2025/9kr7_62521.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kr7_62521/09_2025/9kr7_62521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kr7_62521/09_2025/9kr7_62521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kr7_62521/09_2025/9kr7_62521.map" model { file = "/net/cci-nas-00/data/ceres_data/9kr7_62521/09_2025/9kr7_62521.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kr7_62521/09_2025/9kr7_62521.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.048 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: 5 Type Number sf(0) Gaussians S 37 5.16 5 Cl 1 4.86 5 C 2858 2.51 5 N 658 2.21 5 O 707 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4261 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4253 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 24, 'TRANS': 509} Chain breaks: 1 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1, 'water': 7} Link IDs: {None: 7} Time building chain proxies: 1.40, per 1000 atoms: 0.33 Number of scatterers: 4261 At special positions: 0 Unit cell: (84.4, 68.575, 88.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 37 16.00 O 707 8.00 N 658 7.00 C 2858 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 181 " 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: 0.28 Conformation dependent library (CDL) restraints added in 151.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 1 sheets defined 80.0% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 57 through 70 removed outlier: 4.410A pdb=" N PHE A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 76 removed outlier: 3.555A pdb=" N VAL A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 86 Processing helix chain 'A' and resid 86 through 101 removed outlier: 3.514A pdb=" N PHE A 90 " --> pdb=" O GLY A 86 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 91 " --> pdb=" O GLY A 87 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) Proline residue: A 93 - end of helix Processing helix chain 'A' and resid 101 through 117 Processing helix chain 'A' and resid 121 through 130 removed outlier: 3.863A pdb=" N ILE A 126 " --> pdb=" O VAL A 123 " (cutoff:3.500A) Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 131 through 163 removed outlier: 3.595A pdb=" N TYR A 135 " --> pdb=" O LYS A 131 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE A 149 " --> pdb=" O ASN A 145 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N MET A 150 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 152 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 171 removed outlier: 3.924A pdb=" N THR A 171 " --> pdb=" O PRO A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 232 through 253 removed outlier: 3.548A pdb=" N CYS A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 281 removed outlier: 3.574A pdb=" N THR A 264 " --> pdb=" O ILE A 260 " (cutoff:3.500A) Proline residue: A 268 - end of helix Processing helix chain 'A' and resid 284 through 294 removed outlier: 3.622A pdb=" N GLY A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 300 Processing helix chain 'A' and resid 302 through 317 removed outlier: 4.240A pdb=" N TRP A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 331 removed outlier: 3.620A pdb=" N ALA A 326 " --> pdb=" O GLY A 322 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 371 removed outlier: 3.656A pdb=" N ILE A 362 " --> pdb=" O VAL A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 377 removed outlier: 3.517A pdb=" N VAL A 377 " --> pdb=" O ILE A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 386 Processing helix chain 'A' and resid 387 through 394 removed outlier: 3.531A pdb=" N ARG A 391 " --> pdb=" O ILE A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 433 Processing helix chain 'A' and resid 441 through 459 Processing helix chain 'A' and resid 465 through 476 removed outlier: 4.224A pdb=" N VAL A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 496 removed outlier: 3.525A pdb=" N LEU A 484 " --> pdb=" O GLY A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 512 Processing helix chain 'A' and resid 516 through 525 removed outlier: 4.161A pdb=" N LYS A 520 " --> pdb=" O CYS A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 541 Processing helix chain 'A' and resid 554 through 570 Processing helix chain 'A' and resid 570 through 583 Processing helix chain 'A' and resid 586 through 595 Processing sheet with id=AA1, first strand: chain 'A' and resid 546 through 547 283 hydrogen bonds defined for protein. 822 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: 0.63 Time building geometry restraints manager: 0.40 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: 1236 1.34 - 1.46: 1176 1.46 - 1.58: 1934 1.58 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 4400 Sorted by residual: bond pdb=" N ASN A 85 " pdb=" CA ASN A 85 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.32e-02 5.74e+03 6.75e+00 bond pdb=" N TYR A 80 " pdb=" CA TYR A 80 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.19e-02 7.06e+03 6.63e+00 bond pdb=" N VAL A 75 " pdb=" CA VAL A 75 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.34e-02 5.57e+03 6.52e+00 bond pdb=" N ARG A 77 " pdb=" CA ARG A 77 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.20e-02 6.94e+03 6.28e+00 bond pdb=" N TYR A 83 " pdb=" CA TYR A 83 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.22e+00 ... (remaining 4395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 5785 1.28 - 2.57: 170 2.57 - 3.85: 42 3.85 - 5.13: 9 5.13 - 6.41: 4 Bond angle restraints: 6010 Sorted by residual: angle pdb=" CA ARG A 77 " pdb=" C ARG A 77 " pdb=" O ARG A 77 " ideal model delta sigma weight residual 120.70 117.82 2.88 1.03e+00 9.43e-01 7.82e+00 angle pdb=" N LEU A 72 " pdb=" CA LEU A 72 " pdb=" C LEU A 72 " ideal model delta sigma weight residual 112.89 109.46 3.43 1.24e+00 6.50e-01 7.66e+00 angle pdb=" CA CYS A 82 " pdb=" C CYS A 82 " pdb=" O CYS A 82 " ideal model delta sigma weight residual 120.82 118.03 2.79 1.05e+00 9.07e-01 7.08e+00 angle pdb=" N GLY A 73 " pdb=" CA GLY A 73 " pdb=" C GLY A 73 " ideal model delta sigma weight residual 114.16 111.05 3.11 1.21e+00 6.83e-01 6.62e+00 angle pdb=" C TYR A 80 " pdb=" CA TYR A 80 " pdb=" CB TYR A 80 " ideal model delta sigma weight residual 110.88 114.84 -3.96 1.57e+00 4.06e-01 6.37e+00 ... (remaining 6005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 2230 17.67 - 35.33: 187 35.33 - 53.00: 23 53.00 - 70.66: 6 70.66 - 88.33: 3 Dihedral angle restraints: 2449 sinusoidal: 915 harmonic: 1534 Sorted by residual: dihedral pdb=" CD ARG A 77 " pdb=" NE ARG A 77 " pdb=" CZ ARG A 77 " pdb=" NH1 ARG A 77 " ideal model delta sinusoidal sigma weight residual 0.00 -29.22 29.22 1 1.00e+01 1.00e-02 1.22e+01 dihedral pdb=" CB GLU A 423 " pdb=" CG GLU A 423 " pdb=" CD GLU A 423 " pdb=" OE1 GLU A 423 " ideal model delta sinusoidal sigma weight residual 0.00 88.33 -88.33 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU A 558 " pdb=" CG GLU A 558 " pdb=" CD GLU A 558 " pdb=" OE1 GLU A 558 " ideal model delta sinusoidal sigma weight residual 0.00 -86.37 86.37 1 3.00e+01 1.11e-03 9.99e+00 ... (remaining 2446 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 450 0.038 - 0.076: 161 0.076 - 0.114: 39 0.114 - 0.152: 6 0.152 - 0.190: 1 Chirality restraints: 657 Sorted by residual: chirality pdb=" CA VAL A 75 " pdb=" N VAL A 75 " pdb=" C VAL A 75 " pdb=" CB VAL A 75 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CA ASN A 74 " pdb=" N ASN A 74 " pdb=" C ASN A 74 " pdb=" CB ASN A 74 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA THR A 527 " pdb=" N THR A 527 " pdb=" C THR A 527 " pdb=" CB THR A 527 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.12 2.00e-01 2.50e+01 3.90e-01 ... (remaining 654 not shown) Planarity restraints: 730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 77 " -0.525 9.50e-02 1.11e+02 2.36e-01 3.40e+01 pdb=" NE ARG A 77 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG A 77 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 77 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 77 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 151 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.13e+00 pdb=" C VAL A 151 " -0.025 2.00e-02 2.50e+03 pdb=" O VAL A 151 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU A 152 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 381 " 0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO A 382 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 382 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 382 " 0.020 5.00e-02 4.00e+02 ... (remaining 727 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 342 2.74 - 3.28: 4525 3.28 - 3.82: 7401 3.82 - 4.36: 8578 4.36 - 4.90: 14993 Nonbonded interactions: 35839 Sorted by model distance: nonbonded pdb=" OD1 ASP A 60 " pdb=" OH TYR A 262 " model vdw 2.195 3.040 nonbonded pdb=" OG1 THR A 586 " pdb=" OE1 GLU A 589 " model vdw 2.213 3.040 nonbonded pdb=" O ASN A 232 " pdb=" OG1 THR A 236 " model vdw 2.262 3.040 nonbonded pdb=" OH TYR A 269 " pdb=" OG1 THR A 351 " model vdw 2.270 3.040 nonbonded pdb=" O SER A 316 " pdb=" O HOH A 801 " model vdw 2.282 3.040 ... (remaining 35834 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: 0.930 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.150 Find NCS groups from input model: 0.150 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4401 Z= 0.227 Angle : 0.566 6.414 6012 Z= 0.321 Chirality : 0.040 0.190 657 Planarity : 0.010 0.236 730 Dihedral : 13.528 88.330 1474 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.22 % Allowed : 0.67 % Favored : 99.10 % 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 aren not related in a simple way. whole: 0.41 (0.37), residues: 530 helix: 0.71 (0.27), residues: 366 sheet: None (None), residues: 0 loop : -0.54 (0.54), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 77 TYR 0.013 0.001 TYR A 80 PHE 0.012 0.001 PHE A 106 TRP 0.016 0.001 TRP A 555 HIS 0.002 0.001 HIS A 603 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 4400) covalent geometry : angle 0.56555 ( 6010) SS BOND : bond 0.00230 ( 1) SS BOND : angle 0.72574 ( 2) hydrogen bonds : bond 0.15335 ( 283) hydrogen bonds : angle 6.82725 ( 822) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.136 Fit side-chains REVERT: A 464 ASP cc_start: 0.8812 (m-30) cc_final: 0.8550 (m-30) outliers start: 1 outliers final: 1 residues processed: 76 average time/residue: 0.0552 time to fit residues: 5.7051 Evaluate side-chains 66 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.0670 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 ASN ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.130907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.109025 restraints weight = 5531.984| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.50 r_work: 0.3019 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4401 Z= 0.141 Angle : 0.521 5.554 6012 Z= 0.269 Chirality : 0.039 0.134 657 Planarity : 0.004 0.037 730 Dihedral : 4.356 49.932 579 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.57 % Allowed : 6.28 % Favored : 92.15 % 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 aren not related in a simple way. whole: 1.46 (0.38), residues: 530 helix: 1.55 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -0.37 (0.55), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 590 TYR 0.018 0.001 TYR A 148 PHE 0.016 0.001 PHE A 115 TRP 0.013 0.001 TRP A 485 HIS 0.002 0.001 HIS A 603 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 4400) covalent geometry : angle 0.52093 ( 6010) SS BOND : bond 0.00327 ( 1) SS BOND : angle 1.38986 ( 2) hydrogen bonds : bond 0.04474 ( 283) hydrogen bonds : angle 4.38119 ( 822) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.096 Fit side-chains REVERT: A 115 PHE cc_start: 0.8824 (t80) cc_final: 0.8599 (t80) REVERT: A 464 ASP cc_start: 0.8734 (m-30) cc_final: 0.8440 (m-30) outliers start: 7 outliers final: 6 residues processed: 72 average time/residue: 0.0493 time to fit residues: 4.8678 Evaluate side-chains 70 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 187 HIS Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 529 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 chunk 47 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 0.0020 chunk 7 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.131118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.109143 restraints weight = 5435.789| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.53 r_work: 0.3014 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4401 Z= 0.131 Angle : 0.512 7.788 6012 Z= 0.259 Chirality : 0.038 0.127 657 Planarity : 0.004 0.036 730 Dihedral : 4.291 51.010 579 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.47 % Allowed : 8.97 % Favored : 88.57 % 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 aren not related in a simple way. whole: 1.75 (0.38), residues: 530 helix: 1.78 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -0.27 (0.55), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 502 TYR 0.015 0.001 TYR A 148 PHE 0.013 0.001 PHE A 115 TRP 0.012 0.001 TRP A 485 HIS 0.002 0.001 HIS A 603 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 4400) covalent geometry : angle 0.51133 ( 6010) SS BOND : bond 0.00303 ( 1) SS BOND : angle 1.15823 ( 2) hydrogen bonds : bond 0.04192 ( 283) hydrogen bonds : angle 4.18526 ( 822) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.142 Fit side-chains REVERT: A 115 PHE cc_start: 0.8785 (t80) cc_final: 0.8548 (t80) REVERT: A 464 ASP cc_start: 0.8754 (m-30) cc_final: 0.8412 (m-30) outliers start: 11 outliers final: 8 residues processed: 74 average time/residue: 0.0474 time to fit residues: 4.7301 Evaluate side-chains 74 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 187 HIS Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 529 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 4 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 2 optimal weight: 0.3980 chunk 12 optimal weight: 0.0470 chunk 15 optimal weight: 0.0070 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.134958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.113604 restraints weight = 5395.952| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.48 r_work: 0.3069 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4401 Z= 0.105 Angle : 0.483 6.902 6012 Z= 0.243 Chirality : 0.037 0.120 657 Planarity : 0.003 0.033 730 Dihedral : 4.179 52.058 579 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.24 % Allowed : 9.19 % Favored : 88.57 % 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 aren not related in a simple way. whole: 1.94 (0.38), residues: 530 helix: 1.95 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -0.32 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 278 TYR 0.015 0.001 TYR A 148 PHE 0.011 0.001 PHE A 115 TRP 0.012 0.001 TRP A 555 HIS 0.005 0.001 HIS A 575 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 4400) covalent geometry : angle 0.48248 ( 6010) SS BOND : bond 0.00253 ( 1) SS BOND : angle 0.99112 ( 2) hydrogen bonds : bond 0.03715 ( 283) hydrogen bonds : angle 3.98550 ( 822) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.163 Fit side-chains REVERT: A 80 TYR cc_start: 0.8071 (OUTLIER) cc_final: 0.7196 (t80) REVERT: A 115 PHE cc_start: 0.8775 (t80) cc_final: 0.8434 (t80) REVERT: A 150 MET cc_start: 0.8871 (tpp) cc_final: 0.8515 (tpt) REVERT: A 357 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7559 (t80) REVERT: A 504 MET cc_start: 0.8643 (mmm) cc_final: 0.8400 (mmm) outliers start: 10 outliers final: 7 residues processed: 72 average time/residue: 0.0594 time to fit residues: 5.7917 Evaluate side-chains 76 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 187 HIS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 529 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 32 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 25 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 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.132679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.110191 restraints weight = 5447.021| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.58 r_work: 0.3017 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4401 Z= 0.132 Angle : 0.495 7.046 6012 Z= 0.249 Chirality : 0.038 0.125 657 Planarity : 0.004 0.033 730 Dihedral : 4.216 52.463 579 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.69 % Allowed : 10.76 % Favored : 86.55 % 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 aren not related in a simple way. whole: 1.89 (0.38), residues: 530 helix: 1.92 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -0.38 (0.54), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 502 TYR 0.015 0.001 TYR A 80 PHE 0.019 0.001 PHE A 248 TRP 0.014 0.001 TRP A 555 HIS 0.003 0.001 HIS A 575 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 4400) covalent geometry : angle 0.49441 ( 6010) SS BOND : bond 0.00243 ( 1) SS BOND : angle 0.98030 ( 2) hydrogen bonds : bond 0.03876 ( 283) hydrogen bonds : angle 4.00589 ( 822) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.126 Fit side-chains REVERT: A 115 PHE cc_start: 0.8942 (t80) cc_final: 0.8569 (t80) REVERT: A 357 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7603 (t80) REVERT: A 504 MET cc_start: 0.8610 (mmm) cc_final: 0.8378 (mmm) outliers start: 12 outliers final: 9 residues processed: 73 average time/residue: 0.0496 time to fit residues: 5.0132 Evaluate side-chains 73 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 187 HIS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 529 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.129990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.107648 restraints weight = 5539.018| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.57 r_work: 0.2999 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4401 Z= 0.154 Angle : 0.511 6.114 6012 Z= 0.257 Chirality : 0.039 0.127 657 Planarity : 0.004 0.034 730 Dihedral : 4.301 53.836 579 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.14 % Allowed : 11.21 % Favored : 85.65 % 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 aren not related in a simple way. whole: 1.76 (0.38), residues: 530 helix: 1.80 (0.27), residues: 379 sheet: None (None), residues: 0 loop : -0.42 (0.55), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 502 TYR 0.016 0.001 TYR A 80 PHE 0.014 0.001 PHE A 248 TRP 0.014 0.001 TRP A 555 HIS 0.002 0.001 HIS A 575 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 4400) covalent geometry : angle 0.51031 ( 6010) SS BOND : bond 0.00266 ( 1) SS BOND : angle 1.03504 ( 2) hydrogen bonds : bond 0.04036 ( 283) hydrogen bonds : angle 4.06553 ( 822) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.160 Fit side-chains REVERT: A 115 PHE cc_start: 0.8884 (t80) cc_final: 0.8523 (t80) REVERT: A 150 MET cc_start: 0.8937 (tpp) cc_final: 0.8589 (tpt) REVERT: A 357 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7622 (t80) REVERT: A 504 MET cc_start: 0.8624 (mmm) cc_final: 0.8407 (mmm) REVERT: A 538 ASN cc_start: 0.7881 (OUTLIER) cc_final: 0.7560 (m-40) outliers start: 14 outliers final: 9 residues processed: 77 average time/residue: 0.0562 time to fit residues: 5.9005 Evaluate side-chains 74 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 187 HIS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 538 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 34 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 1 optimal weight: 0.0980 chunk 31 optimal weight: 0.3980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.131498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.108879 restraints weight = 5492.585| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.60 r_work: 0.3013 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4401 Z= 0.122 Angle : 0.497 6.954 6012 Z= 0.249 Chirality : 0.038 0.124 657 Planarity : 0.004 0.034 730 Dihedral : 4.262 54.536 579 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.91 % Allowed : 12.56 % Favored : 84.53 % 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 aren not related in a simple way. whole: 1.73 (0.38), residues: 530 helix: 1.73 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -0.37 (0.56), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 502 TYR 0.014 0.001 TYR A 80 PHE 0.013 0.001 PHE A 248 TRP 0.016 0.001 TRP A 555 HIS 0.003 0.001 HIS A 575 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 4400) covalent geometry : angle 0.49709 ( 6010) SS BOND : bond 0.00256 ( 1) SS BOND : angle 1.06213 ( 2) hydrogen bonds : bond 0.03835 ( 283) hydrogen bonds : angle 4.01797 ( 822) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.168 Fit side-chains REVERT: A 115 PHE cc_start: 0.8842 (t80) cc_final: 0.8464 (t80) REVERT: A 150 MET cc_start: 0.8937 (tpp) cc_final: 0.8680 (tpt) REVERT: A 357 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7567 (t80) REVERT: A 413 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7798 (mp) REVERT: A 504 MET cc_start: 0.8602 (mmm) cc_final: 0.8399 (mmm) REVERT: A 538 ASN cc_start: 0.7847 (OUTLIER) cc_final: 0.7548 (m-40) outliers start: 13 outliers final: 9 residues processed: 72 average time/residue: 0.0503 time to fit residues: 4.9607 Evaluate side-chains 75 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 187 HIS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 538 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 14 optimal weight: 0.0980 chunk 21 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 12 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 4 optimal weight: 0.0170 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.131599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.109240 restraints weight = 5460.842| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.55 r_work: 0.3022 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4401 Z= 0.122 Angle : 0.489 6.286 6012 Z= 0.245 Chirality : 0.038 0.123 657 Planarity : 0.003 0.033 730 Dihedral : 4.246 54.907 579 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.36 % Allowed : 13.00 % Favored : 83.63 % 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 aren not related in a simple way. whole: 1.80 (0.38), residues: 530 helix: 1.80 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -0.37 (0.56), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 502 TYR 0.014 0.001 TYR A 80 PHE 0.012 0.001 PHE A 248 TRP 0.019 0.001 TRP A 555 HIS 0.003 0.001 HIS A 575 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 4400) covalent geometry : angle 0.48848 ( 6010) SS BOND : bond 0.00243 ( 1) SS BOND : angle 0.98205 ( 2) hydrogen bonds : bond 0.03779 ( 283) hydrogen bonds : angle 3.99256 ( 822) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.164 Fit side-chains REVERT: A 115 PHE cc_start: 0.8829 (t80) cc_final: 0.8464 (t80) REVERT: A 150 MET cc_start: 0.8932 (tpp) cc_final: 0.8712 (tpt) REVERT: A 357 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7520 (t80) REVERT: A 413 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7661 (mp) REVERT: A 538 ASN cc_start: 0.7801 (OUTLIER) cc_final: 0.7498 (m-40) outliers start: 15 outliers final: 10 residues processed: 77 average time/residue: 0.0573 time to fit residues: 5.9756 Evaluate side-chains 76 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 187 HIS Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 538 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.0970 chunk 25 optimal weight: 0.1980 chunk 32 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 18 optimal weight: 0.0870 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.133400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.110778 restraints weight = 5484.593| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.59 r_work: 0.3046 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4401 Z= 0.114 Angle : 0.504 8.050 6012 Z= 0.253 Chirality : 0.038 0.121 657 Planarity : 0.004 0.033 730 Dihedral : 4.262 55.027 579 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.59 % Allowed : 12.78 % Favored : 83.63 % 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 aren not related in a simple way. whole: 1.90 (0.38), residues: 530 helix: 1.85 (0.27), residues: 384 sheet: None (None), residues: 0 loop : -0.27 (0.56), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 502 TYR 0.013 0.001 TYR A 80 PHE 0.012 0.001 PHE A 248 TRP 0.024 0.001 TRP A 555 HIS 0.003 0.001 HIS A 575 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 4400) covalent geometry : angle 0.50395 ( 6010) SS BOND : bond 0.00234 ( 1) SS BOND : angle 1.07041 ( 2) hydrogen bonds : bond 0.03681 ( 283) hydrogen bonds : angle 3.97444 ( 822) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.155 Fit side-chains REVERT: A 115 PHE cc_start: 0.8799 (t80) cc_final: 0.8436 (t80) REVERT: A 150 MET cc_start: 0.8905 (tpp) cc_final: 0.8644 (tpt) REVERT: A 248 PHE cc_start: 0.8548 (t80) cc_final: 0.8319 (t80) REVERT: A 357 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7492 (t80) REVERT: A 413 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7756 (mp) REVERT: A 538 ASN cc_start: 0.7840 (OUTLIER) cc_final: 0.7549 (m-40) outliers start: 16 outliers final: 9 residues processed: 75 average time/residue: 0.0523 time to fit residues: 5.3323 Evaluate side-chains 76 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 538 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 17 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 0.2980 chunk 1 optimal weight: 0.6980 chunk 12 optimal weight: 10.0000 chunk 2 optimal weight: 0.5980 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 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.131518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.109001 restraints weight = 5497.951| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.58 r_work: 0.3024 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4401 Z= 0.138 Angle : 0.528 7.564 6012 Z= 0.265 Chirality : 0.039 0.124 657 Planarity : 0.004 0.033 730 Dihedral : 4.315 54.902 579 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.91 % Allowed : 13.68 % Favored : 83.41 % 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 aren not related in a simple way. whole: 1.82 (0.38), residues: 530 helix: 1.79 (0.27), residues: 384 sheet: None (None), residues: 0 loop : -0.28 (0.57), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 590 TYR 0.015 0.001 TYR A 80 PHE 0.011 0.001 PHE A 248 TRP 0.026 0.001 TRP A 555 HIS 0.002 0.000 HIS A 575 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 4400) covalent geometry : angle 0.52724 ( 6010) SS BOND : bond 0.00244 ( 1) SS BOND : angle 1.07635 ( 2) hydrogen bonds : bond 0.03852 ( 283) hydrogen bonds : angle 4.02694 ( 822) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.153 Fit side-chains REVERT: A 115 PHE cc_start: 0.8802 (t80) cc_final: 0.8431 (t80) REVERT: A 248 PHE cc_start: 0.8576 (t80) cc_final: 0.8361 (t80) REVERT: A 357 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7498 (t80) REVERT: A 413 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7639 (mp) REVERT: A 538 ASN cc_start: 0.7883 (OUTLIER) cc_final: 0.7567 (m-40) outliers start: 13 outliers final: 10 residues processed: 71 average time/residue: 0.0566 time to fit residues: 5.4552 Evaluate side-chains 75 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 538 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 42 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 44 optimal weight: 0.1980 chunk 17 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 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 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.131897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.109282 restraints weight = 5432.294| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.59 r_work: 0.3017 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4401 Z= 0.138 Angle : 0.532 7.547 6012 Z= 0.266 Chirality : 0.039 0.124 657 Planarity : 0.004 0.033 730 Dihedral : 4.335 55.308 579 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.14 % Allowed : 13.45 % Favored : 83.41 % 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 aren not related in a simple way. whole: 1.84 (0.38), residues: 530 helix: 1.80 (0.27), residues: 384 sheet: None (None), residues: 0 loop : -0.27 (0.57), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 502 TYR 0.015 0.001 TYR A 80 PHE 0.011 0.001 PHE A 248 TRP 0.025 0.001 TRP A 555 HIS 0.002 0.000 HIS A 575 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 4400) covalent geometry : angle 0.53132 ( 6010) SS BOND : bond 0.00251 ( 1) SS BOND : angle 1.08387 ( 2) hydrogen bonds : bond 0.03873 ( 283) hydrogen bonds : angle 4.03474 ( 822) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1152.07 seconds wall clock time: 20 minutes 26.49 seconds (1226.49 seconds total)