Starting phenix.real_space_refine on Wed Jul 1 23:42:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kr7_62521/07_2026/9kr7_62521.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kr7_62521/07_2026/9kr7_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 { model { file = "/net/cci-nas-00/data/ceres_data/9kr7_62521/07_2026/9kr7_62521.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kr7_62521/07_2026/9kr7_62521.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kr7_62521/07_2026/9kr7_62521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kr7_62521/07_2026/9kr7_62521.map" } 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-dev-6108/lib/python3.11/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, 7 Ad-hoc single atom residues: {' CL': 1} Classifications: {'water': 7} Link IDs: {None: 6} Chain breaks: 1 Time building chain proxies: 0.97, per 1000 atoms: 0.23 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: 0.21 Conformation dependent library (CDL) restraints added in 93.2 milliseconds 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: 0.12 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: 0.59 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: 1.22 - 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.860 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 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 are 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/Z covalent geometry : bond 0.00439 / 0.23 ( 4400) covalent geometry : angle 0.56555 / 0.32 ( 6010) SS BOND : bond 0.00230 / 0.12 ( 1) SS BOND : angle 0.72574 / 0.39 ( 2) hydrogen bonds : bond 0.15335 / 9.68 ( 283) hydrogen bonds : angle 6.82725 / 4.83 ( 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 : 0.186 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: 0.0519 time to fit residues: 5.4247 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 : 0.090 ------------------------------------------------------------------------------- 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: 0.9990 chunk 48 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3373 r_free = 0.3373 target = 0.129219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.107419 restraints weight = 5528.756| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.53 r_work: 0.3006 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4401 Z= 0.154 Angle : 0.533 5.537 6012 Z= 0.275 Chirality : 0.039 0.136 657 Planarity : 0.004 0.038 730 Dihedral : 4.394 50.155 579 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.57 % Allowed : 6.73 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.38), residues: 530 helix: 1.53 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -0.39 (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 0.017 0.001 PHE A 115 TRP 0.014 0.001 TRP A 76 HIS 0.002 0.001 HIS A 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 ( 4400) covalent geometry : angle 0.53267 / 0.27 ( 6010) SS BOND : bond 0.00348 / 0.18 ( 1) SS BOND : angle 1.44333 / 0.76 ( 2) hydrogen bonds : bond 0.04567 / 3.08 ( 283) hydrogen bonds : angle 4.40975 / 3.16 ( 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 77 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.148 Fit side-chains REVERT: A 115 PHE cc_start: 0.8851 (t80) cc_final: 0.8616 (t80) REVERT: A 464 ASP cc_start: 0.8716 (m-30) cc_final: 0.8443 (m-30) outliers start: 7 outliers final: 6 residues processed: 73 average time/residue: 0.0513 time to fit residues: 5.1267 Evaluate side-chains 69 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.107 ------------------------------------------------------------------------------- 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: 0.6980 chunk 47 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3374 r_free = 0.3374 target = 0.129164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.107155 restraints weight = 5449.853| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.53 r_work: 0.2985 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4401 Z= 0.161 Angle : 0.531 5.580 6012 Z= 0.271 Chirality : 0.039 0.130 657 Planarity : 0.004 0.036 730 Dihedral : 4.385 51.716 579 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.69 % Allowed : 7.85 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.38), residues: 530 helix: 1.68 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -0.30 (0.55), residues: 156 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 0.013 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/Z covalent geometry : bond 0.00385 / 0.16 ( 4400) covalent geometry : angle 0.53100 / 0.27 ( 6010) SS BOND : bond 0.00311 / 0.16 ( 1) SS BOND : angle 1.21161 / 0.62 ( 2) hydrogen bonds : bond 0.04394 / 2.96 ( 283) hydrogen bonds : angle 4.26472 / 3.06 ( 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 79 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.150 Fit side-chains REVERT: A 115 PHE cc_start: 0.8804 (t80) cc_final: 0.8554 (t80) REVERT: A 464 ASP cc_start: 0.8811 (m-30) cc_final: 0.8450 (m-30) outliers start: 12 outliers final: 9 residues processed: 72 average time/residue: 0.0531 time to fit residues: 5.1862 Evaluate side-chains 74 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.116 ------------------------------------------------------------------------------- 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 357 PHE 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: 0.8980 chunk 41 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3369 r_free = 0.3369 target = 0.128904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.106573 restraints weight = 5450.896| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.55 r_work: 0.2984 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4401 Z= 0.154 Angle : 0.526 6.743 6012 Z= 0.266 Chirality : 0.039 0.127 657 Planarity : 0.004 0.035 730 Dihedral : 4.392 53.859 579 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.69 % Allowed : 9.87 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.38), residues: 530 helix: 1.71 (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 502 TYR 0.016 0.001 TYR A 80 PHE 0.012 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/Z covalent geometry : bond 0.00369 / 0.15 ( 4400) covalent geometry : angle 0.52594 / 0.27 ( 6010) SS BOND : bond 0.00280 / 0.15 ( 1) SS BOND : angle 1.09337 / 0.57 ( 2) hydrogen bonds : bond 0.04173 / 2.83 ( 283) hydrogen bonds : angle 4.15747 / 3.00 ( 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: 12 poor density : 66 time to evaluate : 0.156 Fit side-chains REVERT: A 115 PHE cc_start: 0.8878 (t80) cc_final: 0.8630 (t80) outliers start: 12 outliers final: 9 residues processed: 71 average time/residue: 0.0563 time to fit residues: 5.4683 Evaluate side-chains 75 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.164 ------------------------------------------------------------------------------- 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: 0.3980 chunk 45 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3373 r_free = 0.3373 target = 0.129401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.107168 restraints weight = 5448.088| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.53 r_work: 0.2995 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4401 Z= 0.138 Angle : 0.506 5.561 6012 Z= 0.255 Chirality : 0.038 0.127 657 Planarity : 0.004 0.034 730 Dihedral : 4.352 54.584 579 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.91 % Allowed : 10.09 % Favored : 87.00 % 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: 1.73 (0.38), residues: 530 helix: 1.78 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -0.38 (0.55), residues: 155 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 0.020 0.001 PHE A 248 TRP 0.012 0.001 TRP A 485 HIS 0.002 0.001 HIS A 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 4400) covalent geometry : angle 0.50578 / 0.25 ( 6010) SS BOND : bond 0.00273 / 0.14 ( 1) SS BOND : angle 1.08614 / 0.57 ( 2) hydrogen bonds : bond 0.04040 / 2.74 ( 283) hydrogen bonds : angle 4.09415 / 2.96 ( 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 79 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.188 Fit side-chains REVERT: A 115 PHE cc_start: 0.8858 (t80) cc_final: 0.8632 (t80) REVERT: A 150 MET cc_start: 0.8949 (tpp) cc_final: 0.8583 (tpt) REVERT: A 504 MET cc_start: 0.8602 (mmm) cc_final: 0.8377 (mmm) REVERT: A 538 ASN cc_start: 0.7910 (OUTLIER) cc_final: 0.7587 (m-40) outliers start: 13 outliers final: 10 residues processed: 74 average time/residue: 0.0571 time to fit residues: 5.7314 Evaluate side-chains 76 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.107 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 30 optimal weight: 0.4980 chunk 13 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3368 r_free = 0.3368 target = 0.128946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.106535 restraints weight = 5535.952| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.55 r_work: 0.2992 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4401 Z= 0.143 Angle : 0.510 6.785 6012 Z= 0.256 Chirality : 0.038 0.127 657 Planarity : 0.004 0.034 730 Dihedral : 4.358 55.014 579 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % 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 are not related in a simple way. whole: 1.83 (0.38), residues: 530 helix: 1.85 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -0.29 (0.54), residues: 156 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 0.013 0.001 TRP A 555 HIS 0.002 0.001 HIS A 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 ( 4400) covalent geometry : angle 0.50924 / 0.26 ( 6010) SS BOND : bond 0.00250 / 0.13 ( 1) SS BOND : angle 1.04818 / 0.55 ( 2) hydrogen bonds : bond 0.04025 / 2.74 ( 283) hydrogen bonds : angle 4.09037 / 2.96 ( 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 80 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.173 Fit side-chains REVERT: A 115 PHE cc_start: 0.8826 (t80) cc_final: 0.8566 (t80) REVERT: A 357 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.7491 (t80) REVERT: A 504 MET cc_start: 0.8577 (mmm) cc_final: 0.8363 (mmm) REVERT: A 538 ASN cc_start: 0.7909 (OUTLIER) cc_final: 0.7610 (m-40) outliers start: 14 outliers final: 9 residues processed: 75 average time/residue: 0.0497 time to fit residues: 5.1208 Evaluate side-chains 76 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.115 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 43 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3374 r_free = 0.3374 target = 0.129360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.107014 restraints weight = 5503.209| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.57 r_work: 0.2991 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1691 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= 0.148 Angle : 0.521 6.056 6012 Z= 0.262 Chirality : 0.039 0.127 657 Planarity : 0.004 0.034 730 Dihedral : 4.384 55.432 579 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.36 % Allowed : 11.43 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.38), residues: 530 helix: 1.78 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -0.37 (0.55), residues: 152 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 0.013 0.001 PHE A 248 TRP 0.013 0.001 TRP A 555 HIS 0.002 0.001 HIS A 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 4400) covalent geometry : angle 0.52113 / 0.26 ( 6010) SS BOND : bond 0.00269 / 0.14 ( 1) SS BOND : angle 1.10014 / 0.57 ( 2) hydrogen bonds : bond 0.04022 / 2.74 ( 283) hydrogen bonds : angle 4.10459 / 2.97 ( 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 80 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.163 Fit side-chains REVERT: A 115 PHE cc_start: 0.8839 (t80) cc_final: 0.8577 (t80) REVERT: A 150 MET cc_start: 0.8898 (tpp) cc_final: 0.8593 (tpt) REVERT: A 357 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7475 (t80) REVERT: A 538 ASN cc_start: 0.7950 (OUTLIER) cc_final: 0.7645 (m-40) outliers start: 15 outliers final: 10 residues processed: 75 average time/residue: 0.0544 time to fit residues: 5.6170 Evaluate side-chains 77 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 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 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: 0.7980 chunk 21 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 7 optimal weight: 0.3980 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 4 optimal weight: 0.0170 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3378 r_free = 0.3378 target = 0.129766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.107395 restraints weight = 5457.156| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.55 r_work: 0.2999 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1761 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 : 0.509 7.704 6012 Z= 0.254 Chirality : 0.038 0.125 657 Planarity : 0.004 0.034 730 Dihedral : 4.341 55.858 579 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.14 % Allowed : 11.66 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.38), residues: 530 helix: 1.85 (0.27), residues: 377 sheet: None (None), residues: 0 loop : -0.37 (0.55), residues: 153 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 0.013 0.001 PHE A 248 TRP 0.015 0.001 TRP A 555 HIS 0.002 0.001 HIS A 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 4400) covalent geometry : angle 0.50826 / 0.25 ( 6010) SS BOND : bond 0.00276 / 0.15 ( 1) SS BOND : angle 1.23162 / 0.63 ( 2) hydrogen bonds : bond 0.03899 / 2.66 ( 283) hydrogen bonds : angle 4.06014 / 2.93 ( 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 83 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.095 Fit side-chains REVERT: A 115 PHE cc_start: 0.8807 (t80) cc_final: 0.8547 (t80) REVERT: A 150 MET cc_start: 0.8928 (tpp) cc_final: 0.8594 (tpt) REVERT: A 357 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7465 (t80) REVERT: A 538 ASN cc_start: 0.7925 (OUTLIER) cc_final: 0.7626 (m-40) outliers start: 14 outliers final: 10 residues processed: 78 average time/residue: 0.0590 time to fit residues: 6.1684 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 : 0.150 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 34 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 19 optimal weight: 0.0010 chunk 3 optimal weight: 0.0070 chunk 25 optimal weight: 0.3980 chunk 32 optimal weight: 0.3980 chunk 41 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 overall best weight: 0.2804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 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 = 0.3428 r_free = 0.3428 target = 0.133708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.110615 restraints weight = 5477.047| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.63 r_work: 0.3040 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4401 Z= 0.108 Angle : 0.497 7.289 6012 Z= 0.249 Chirality : 0.037 0.121 657 Planarity : 0.004 0.033 730 Dihedral : 4.276 56.073 579 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.91 % Allowed : 12.33 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.38), residues: 530 helix: 1.95 (0.27), residues: 377 sheet: None (None), residues: 0 loop : -0.30 (0.55), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 502 TYR 0.014 0.001 TYR A 147 PHE 0.012 0.001 PHE A 248 TRP 0.021 0.001 TRP A 555 HIS 0.004 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 4400) covalent geometry : angle 0.49658 / 0.25 ( 6010) SS BOND : bond 0.00236 / 0.12 ( 1) SS BOND : angle 1.10608 / 0.58 ( 2) hydrogen bonds : bond 0.03663 / 2.50 ( 283) hydrogen bonds : angle 3.97808 / 2.86 ( 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: 13 poor density : 69 time to evaluate : 0.176 Fit side-chains REVERT: A 115 PHE cc_start: 0.8790 (t80) cc_final: 0.8570 (t80) REVERT: A 150 MET cc_start: 0.8872 (tpp) cc_final: 0.8623 (tpt) REVERT: A 357 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7424 (t80) REVERT: A 538 ASN cc_start: 0.7868 (OUTLIER) cc_final: 0.7559 (m-40) outliers start: 13 outliers final: 9 residues processed: 78 average time/residue: 0.0550 time to fit residues: 5.8560 Evaluate side-chains 77 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 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 208 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 17 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 16 optimal weight: 0.1980 chunk 31 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 ASN A 331 ASN ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.131070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.108464 restraints weight = 5490.711| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.57 r_work: 0.3024 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1956 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 : 0.520 7.222 6012 Z= 0.262 Chirality : 0.038 0.123 657 Planarity : 0.004 0.033 730 Dihedral : 4.325 55.645 579 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.69 % Allowed : 13.45 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.38), residues: 530 helix: 1.92 (0.27), residues: 377 sheet: None (None), residues: 0 loop : -0.33 (0.55), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 590 TYR 0.015 0.001 TYR A 80 PHE 0.018 0.001 PHE A 419 TRP 0.026 0.001 TRP A 555 HIS 0.003 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 4400) covalent geometry : angle 0.51981 / 0.26 ( 6010) SS BOND : bond 0.00267 / 0.14 ( 1) SS BOND : angle 1.15600 / 0.59 ( 2) hydrogen bonds : bond 0.03829 / 2.62 ( 283) hydrogen bonds : angle 4.03098 / 2.91 ( 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 81 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.149 Fit side-chains REVERT: A 115 PHE cc_start: 0.8811 (t80) cc_final: 0.8558 (t80) REVERT: A 150 MET cc_start: 0.8930 (tpp) cc_final: 0.8620 (tpt) REVERT: A 248 PHE cc_start: 0.8522 (t80) cc_final: 0.8270 (t80) REVERT: A 357 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7488 (t80) REVERT: A 538 ASN cc_start: 0.7935 (OUTLIER) cc_final: 0.7617 (m-40) outliers start: 12 outliers final: 9 residues processed: 75 average time/residue: 0.0573 time to fit residues: 5.8486 Evaluate side-chains 76 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 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 208 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 42 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 44 optimal weight: 0.0980 chunk 17 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.131479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.109090 restraints weight = 5436.472| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.56 r_work: 0.3022 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4401 Z= 0.132 Angle : 0.520 7.106 6012 Z= 0.263 Chirality : 0.038 0.124 657 Planarity : 0.004 0.034 730 Dihedral : 4.339 55.899 579 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.69 % Allowed : 13.68 % 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 are not related in a simple way. whole: 1.90 (0.38), residues: 530 helix: 1.92 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -0.31 (0.54), 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 80 PHE 0.015 0.001 PHE A 419 TRP 0.024 0.001 TRP A 555 HIS 0.003 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 4400) covalent geometry : angle 0.51956 / 0.26 ( 6010) SS BOND : bond 0.00232 / 0.12 ( 1) SS BOND : angle 0.98236 / 0.51 ( 2) hydrogen bonds : bond 0.03850 / 2.64 ( 283) hydrogen bonds : angle 4.04483 / 2.92 ( 822) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1173.32 seconds wall clock time: 20 minutes 48.06 seconds (1248.06 seconds total)