Starting phenix.real_space_refine on Thu Jul 2 00:47:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l1b_62740/07_2026/9l1b_62740_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l1b_62740/07_2026/9l1b_62740.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l1b_62740/07_2026/9l1b_62740.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l1b_62740/07_2026/9l1b_62740.map" model { file = "/net/cci-nas-00/data/ceres_data/9l1b_62740/07_2026/9l1b_62740_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l1b_62740/07_2026/9l1b_62740_trim.cif" } resolution = 2.9 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= -0.002 sd= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 33 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 3043 2.51 5 N 681 2.21 5 O 764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 4524 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4415 Classifications: {'peptide': 553} Link IDs: {'PTRANS': 28, 'TRANS': 524} Chain breaks: 1 Chain: "A" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 106 Ad-hoc single atom residues: {' NA': 2, ' CL': 1} Unusual residues: {'CLR': 1, 'TAU': 1, 'Y01': 2} Classifications: {'undetermined': 4, 'water': 1} Link IDs: {None: 4} Chain breaks: 3 Time building chain proxies: 0.93, per 1000 atoms: 0.21 Number of scatterers: 4524 At special positions: 0 Unit cell: (79.92, 71.28, 84.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 33 16.00 Na 2 11.00 O 764 8.00 N 681 7.00 C 3043 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.30 Conformation dependent library (CDL) restraints added in 115.8 milliseconds 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1008 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 1 sheets defined 77.4% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 46 through 59 removed outlier: 3.502A pdb=" N PHE A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.795A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 90 through 106 removed outlier: 3.519A pdb=" N VAL A 94 " --> pdb=" O SER A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 117 removed outlier: 3.674A pdb=" N LYS A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 152 removed outlier: 4.151A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 removed outlier: 4.262A pdb=" N HIS A 161 " --> pdb=" O PRO A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.735A pdb=" N LYS A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 217 through 237 removed outlier: 4.603A pdb=" N LYS A 237 " --> pdb=" O PHE A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 267 removed outlier: 3.768A pdb=" N PHE A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.989A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 286 Processing helix chain 'A' and resid 287 through 302 removed outlier: 4.479A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.808A pdb=" N TYR A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 356 removed outlier: 4.126A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 369 through 379 removed outlier: 3.627A pdb=" N TYR A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Proline residue: A 375 - end of helix Processing helix chain 'A' and resid 383 through 416 removed outlier: 3.573A pdb=" N SER A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 444 removed outlier: 3.828A pdb=" N GLU A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 462 removed outlier: 4.278A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 Processing helix chain 'A' and resid 484 through 497 Processing helix chain 'A' and resid 501 through 510 removed outlier: 4.353A pdb=" N LYS A 505 " --> pdb=" O GLY A 501 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 509 " --> pdb=" O LYS A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 526 Processing helix chain 'A' and resid 539 through 555 removed outlier: 4.153A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 568 Processing helix chain 'A' and resid 571 through 580 Processing helix chain 'A' and resid 586 through 593 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 281 hydrogen bonds defined for protein. 834 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: 0.52 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: 1.18 - 1.31: 661 1.31 - 1.44: 1404 1.44 - 1.57: 2561 1.57 - 1.71: 0 1.71 - 1.84: 47 Bond restraints: 4673 Sorted by residual: bond pdb=" C PRO A 213 " pdb=" O PRO A 213 " ideal model delta sigma weight residual 1.237 1.179 0.059 1.20e-02 6.94e+03 2.39e+01 bond pdb=" N THR A 242 " pdb=" CA THR A 242 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.16e-02 7.43e+03 1.23e+01 bond pdb=" N VAL A 239 " pdb=" CA VAL A 239 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.19e-02 7.06e+03 1.05e+01 bond pdb=" N ARG A 592 " pdb=" CA ARG A 592 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.29e-02 6.01e+03 8.98e+00 bond pdb=" N VAL A 245 " pdb=" CA VAL A 245 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.21e-02 6.83e+03 8.00e+00 ... (remaining 4668 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 6190 2.67 - 5.33: 183 5.33 - 8.00: 11 8.00 - 10.67: 2 10.67 - 13.34: 1 Bond angle restraints: 6387 Sorted by residual: angle pdb=" N PRO A 213 " pdb=" CA PRO A 213 " pdb=" C PRO A 213 " ideal model delta sigma weight residual 113.40 106.78 6.62 1.34e+00 5.57e-01 2.44e+01 angle pdb=" N PRO A 68 " pdb=" CA PRO A 68 " pdb=" C PRO A 68 " ideal model delta sigma weight residual 113.47 120.41 -6.94 1.43e+00 4.89e-01 2.35e+01 angle pdb=" C ARG A 177 " pdb=" N LYS A 178 " pdb=" CA LYS A 178 " ideal model delta sigma weight residual 123.05 116.61 6.44 1.40e+00 5.10e-01 2.11e+01 angle pdb=" O2 TAU A 704 " pdb=" S TAU A 704 " pdb=" O3 TAU A 704 " ideal model delta sigma weight residual 113.11 99.77 13.34 3.00e+00 1.11e-01 1.98e+01 angle pdb=" CA GLY A 214 " pdb=" C GLY A 214 " pdb=" O GLY A 214 " ideal model delta sigma weight residual 122.78 117.94 4.84 1.20e+00 6.94e-01 1.62e+01 ... (remaining 6382 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.45: 2552 23.45 - 46.89: 196 46.89 - 70.34: 36 70.34 - 93.79: 7 93.79 - 117.23: 1 Dihedral angle restraints: 2792 sinusoidal: 1199 harmonic: 1593 Sorted by residual: dihedral pdb=" CBC Y01 A 707 " pdb=" CAR Y01 A 707 " pdb=" CAT Y01 A 707 " pdb=" CBH Y01 A 707 " ideal model delta sinusoidal sigma weight residual -57.13 60.10 -117.23 1 3.00e+01 1.11e-03 1.55e+01 dihedral pdb=" N CYS A 171 " pdb=" C CYS A 171 " pdb=" CA CYS A 171 " pdb=" CB CYS A 171 " ideal model delta harmonic sigma weight residual 122.80 113.83 8.97 0 2.50e+00 1.60e-01 1.29e+01 dihedral pdb=" CAT Y01 A 707 " pdb=" CAR Y01 A 707 " pdb=" CBC Y01 A 707 " pdb=" OAW Y01 A 707 " ideal model delta sinusoidal sigma weight residual 178.96 90.61 88.35 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 2789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 601 0.071 - 0.141: 84 0.141 - 0.212: 12 0.212 - 0.283: 5 0.283 - 0.354: 1 Chirality restraints: 703 Sorted by residual: chirality pdb=" CA CYS A 171 " pdb=" N CYS A 171 " pdb=" C CYS A 171 " pdb=" CB CYS A 171 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CA PRO A 68 " pdb=" N PRO A 68 " pdb=" C PRO A 68 " pdb=" CB PRO A 68 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CG LEU A 306 " pdb=" CB LEU A 306 " pdb=" CD1 LEU A 306 " pdb=" CD2 LEU A 306 " both_signs ideal model delta sigma weight residual False -2.59 -2.83 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 700 not shown) Planarity restraints: 765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 240 " -0.019 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C ARG A 240 " 0.065 2.00e-02 2.50e+03 pdb=" O ARG A 240 " -0.024 2.00e-02 2.50e+03 pdb=" N SER A 241 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 177 " -0.256 9.50e-02 1.11e+02 1.15e-01 8.09e+00 pdb=" NE ARG A 177 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 177 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 177 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 177 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 167 " -0.010 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C ASN A 167 " 0.037 2.00e-02 2.50e+03 pdb=" O ASN A 167 " -0.014 2.00e-02 2.50e+03 pdb=" N THR A 168 " -0.012 2.00e-02 2.50e+03 ... (remaining 762 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 957 2.77 - 3.30: 4561 3.30 - 3.84: 7899 3.84 - 4.37: 9603 4.37 - 4.90: 16265 Nonbonded interactions: 39285 Sorted by model distance: nonbonded pdb=" O SER A 311 " pdb=" OG SER A 314 " model vdw 2.240 3.040 nonbonded pdb=" O LEU A 398 " pdb=" OD1 ASP A 401 " model vdw 2.254 3.040 nonbonded pdb=" O VAL A 59 " pdb="NA NA A 702 " model vdw 2.275 3.210 nonbonded pdb="NA NA A 701 " pdb=" O1 TAU A 704 " model vdw 2.305 3.210 nonbonded pdb=" OD1 ASN A 63 " pdb="NA NA A 701 " model vdw 2.315 3.210 ... (remaining 39280 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.880 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 4674 Z= 0.408 Angle : 0.972 13.337 6389 Z= 0.622 Chirality : 0.054 0.354 703 Planarity : 0.008 0.115 765 Dihedral : 16.580 117.231 1781 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 23.68 % Favored : 76.32 % 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: -0.18 (0.34), residues: 549 helix: 0.40 (0.25), residues: 387 sheet: None (None), residues: 0 loop : -1.20 (0.47), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 583 TYR 0.029 0.001 TYR A 69 PHE 0.013 0.002 PHE A 58 TRP 0.018 0.002 TRP A 218 HIS 0.005 0.002 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00605 / 0.41 ( 4673) covalent geometry : angle 0.97080 / 0.62 ( 6387) SS BOND : bond 0.00492 / 0.33 ( 1) SS BOND : angle 2.57291 / 1.58 ( 2) hydrogen bonds : bond 0.16566 / 10.99 ( 281) hydrogen bonds : angle 7.30185 / 5.40 ( 834) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.167 Fit side-chains REVERT: A 190 ASN cc_start: 0.5855 (m-40) cc_final: 0.5621 (t0) REVERT: A 428 ARG cc_start: 0.7506 (ttt-90) cc_final: 0.6891 (ptp-170) REVERT: A 506 TYR cc_start: 0.7849 (m-10) cc_final: 0.7539 (m-10) REVERT: A 563 ILE cc_start: 0.8776 (mt) cc_final: 0.8556 (mm) REVERT: A 599 ASN cc_start: 0.6677 (p0) cc_final: 0.6397 (p0) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.4492 time to fit residues: 59.9796 Evaluate side-chains 84 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 26 optimal weight: 0.3980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN A 179 ASN A 586 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.123539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.107407 restraints weight = 6425.754| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.76 r_work: 0.3148 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4674 Z= 0.147 Angle : 0.610 6.407 6389 Z= 0.306 Chirality : 0.041 0.195 703 Planarity : 0.004 0.034 765 Dihedral : 8.263 57.484 812 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.81 % Allowed : 21.35 % Favored : 74.84 % 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: 0.85 (0.36), residues: 549 helix: 1.20 (0.27), residues: 387 sheet: None (None), residues: 0 loop : -0.91 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 427 TYR 0.020 0.001 TYR A 69 PHE 0.025 0.002 PHE A 572 TRP 0.018 0.001 TRP A 218 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 4673) covalent geometry : angle 0.60924 / 0.31 ( 6387) SS BOND : bond 0.00329 / 0.22 ( 1) SS BOND : angle 1.41422 / 0.90 ( 2) hydrogen bonds : bond 0.04556 / 3.03 ( 281) hydrogen bonds : angle 4.96259 / 3.79 ( 834) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: A 53 SER cc_start: 0.8751 (m) cc_final: 0.8375 (p) REVERT: A 190 ASN cc_start: 0.5974 (m-40) cc_final: 0.5652 (t0) REVERT: A 286 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7885 (mt-10) REVERT: A 428 ARG cc_start: 0.7710 (ttt-90) cc_final: 0.6593 (ptp-110) REVERT: A 577 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.8034 (tttp) REVERT: A 599 ASN cc_start: 0.7073 (p0) cc_final: 0.6756 (p0) outliers start: 18 outliers final: 10 residues processed: 108 average time/residue: 0.3244 time to fit residues: 37.2500 Evaluate side-chains 94 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 577 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 0.0980 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 31 optimal weight: 0.1980 chunk 30 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 ASN A 202 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.124301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.107415 restraints weight = 6371.426| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.99 r_work: 0.3140 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4674 Z= 0.129 Angle : 0.565 7.384 6389 Z= 0.280 Chirality : 0.040 0.186 703 Planarity : 0.004 0.042 765 Dihedral : 7.396 53.776 812 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.17 % Allowed : 23.04 % Favored : 73.78 % 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: 1.23 (0.36), residues: 549 helix: 1.50 (0.27), residues: 383 sheet: None (None), residues: 0 loop : -0.76 (0.45), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 177 TYR 0.016 0.001 TYR A 69 PHE 0.010 0.001 PHE A 79 TRP 0.013 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 4673) covalent geometry : angle 0.56510 / 0.28 ( 6387) SS BOND : bond 0.00131 / 0.09 ( 1) SS BOND : angle 0.74239 / 0.44 ( 2) hydrogen bonds : bond 0.04218 / 2.80 ( 281) hydrogen bonds : angle 4.78934 / 3.66 ( 834) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: A 53 SER cc_start: 0.8128 (m) cc_final: 0.7621 (p) REVERT: A 190 ASN cc_start: 0.5414 (m-40) cc_final: 0.4966 (t0) REVERT: A 256 MET cc_start: 0.7876 (tpt) cc_final: 0.7600 (tpp) REVERT: A 286 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7572 (mt-10) REVERT: A 428 ARG cc_start: 0.7423 (ttt-90) cc_final: 0.6160 (ptp-110) REVERT: A 577 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.6882 (tppt) REVERT: A 599 ASN cc_start: 0.7285 (p0) cc_final: 0.6958 (p0) outliers start: 15 outliers final: 10 residues processed: 93 average time/residue: 0.3807 time to fit residues: 37.3655 Evaluate side-chains 90 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 577 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 45 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 chunk 51 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 586 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.123057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.106346 restraints weight = 6346.440| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.98 r_work: 0.3130 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4674 Z= 0.135 Angle : 0.563 7.101 6389 Z= 0.276 Chirality : 0.040 0.188 703 Planarity : 0.004 0.035 765 Dihedral : 7.011 52.398 812 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.81 % Allowed : 23.68 % Favored : 72.52 % 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: 1.42 (0.36), residues: 549 helix: 1.66 (0.27), residues: 383 sheet: None (None), residues: 0 loop : -0.73 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 177 TYR 0.021 0.001 TYR A 426 PHE 0.021 0.002 PHE A 572 TRP 0.013 0.001 TRP A 470 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 4673) covalent geometry : angle 0.56292 / 0.28 ( 6387) SS BOND : bond 0.00051 / 0.03 ( 1) SS BOND : angle 0.74104 / 0.46 ( 2) hydrogen bonds : bond 0.04075 / 2.71 ( 281) hydrogen bonds : angle 4.66436 / 3.55 ( 834) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.173 Fit side-chains revert: symmetry clash REVERT: A 53 SER cc_start: 0.8188 (m) cc_final: 0.7678 (p) REVERT: A 190 ASN cc_start: 0.5262 (m-40) cc_final: 0.5009 (t0) REVERT: A 286 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7589 (mt-10) REVERT: A 309 MET cc_start: 0.8804 (mmt) cc_final: 0.8280 (mmp) REVERT: A 428 ARG cc_start: 0.7420 (ttt-90) cc_final: 0.6179 (ptp-110) REVERT: A 599 ASN cc_start: 0.7358 (p0) cc_final: 0.6883 (p0) outliers start: 18 outliers final: 12 residues processed: 89 average time/residue: 0.3262 time to fit residues: 30.8023 Evaluate side-chains 87 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 567 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.0970 chunk 14 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.123610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.106795 restraints weight = 6402.129| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.99 r_work: 0.3146 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4674 Z= 0.124 Angle : 0.544 7.475 6389 Z= 0.268 Chirality : 0.040 0.190 703 Planarity : 0.004 0.035 765 Dihedral : 6.846 50.980 812 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 4.23 % Allowed : 22.83 % Favored : 72.94 % 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: 1.48 (0.37), residues: 549 helix: 1.74 (0.27), residues: 383 sheet: None (None), residues: 0 loop : -0.79 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 177 TYR 0.015 0.001 TYR A 138 PHE 0.014 0.001 PHE A 572 TRP 0.013 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 4673) covalent geometry : angle 0.54418 / 0.27 ( 6387) SS BOND : bond 0.00049 / 0.03 ( 1) SS BOND : angle 0.63677 / 0.39 ( 2) hydrogen bonds : bond 0.03901 / 2.59 ( 281) hydrogen bonds : angle 4.59697 / 3.49 ( 834) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: A 53 SER cc_start: 0.8156 (m) cc_final: 0.7634 (p) REVERT: A 190 ASN cc_start: 0.5284 (m-40) cc_final: 0.5024 (t0) REVERT: A 256 MET cc_start: 0.7872 (tpt) cc_final: 0.7551 (tpp) REVERT: A 428 ARG cc_start: 0.7397 (ttt-90) cc_final: 0.6100 (ptp-110) REVERT: A 599 ASN cc_start: 0.7346 (p0) cc_final: 0.6887 (p0) outliers start: 20 outliers final: 11 residues processed: 87 average time/residue: 0.2918 time to fit residues: 26.9567 Evaluate side-chains 84 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 567 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 21 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 51 optimal weight: 0.0970 chunk 0 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.123055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.106339 restraints weight = 6508.876| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.00 r_work: 0.3141 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4674 Z= 0.129 Angle : 0.548 7.801 6389 Z= 0.268 Chirality : 0.040 0.189 703 Planarity : 0.004 0.034 765 Dihedral : 6.770 49.191 812 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.44 % Allowed : 22.83 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.37), residues: 549 helix: 1.78 (0.27), residues: 384 sheet: None (None), residues: 0 loop : -0.79 (0.47), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 575 TYR 0.021 0.001 TYR A 426 PHE 0.015 0.001 PHE A 458 TRP 0.012 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 4673) covalent geometry : angle 0.54838 / 0.27 ( 6387) SS BOND : bond 0.00053 / 0.04 ( 1) SS BOND : angle 0.62427 / 0.40 ( 2) hydrogen bonds : bond 0.03905 / 2.60 ( 281) hydrogen bonds : angle 4.55454 / 3.45 ( 834) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 53 SER cc_start: 0.8180 (m) cc_final: 0.7662 (p) REVERT: A 190 ASN cc_start: 0.5308 (m-40) cc_final: 0.5029 (t0) REVERT: A 286 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7219 (mm-30) REVERT: A 428 ARG cc_start: 0.7420 (ttt-90) cc_final: 0.6129 (ptp-110) REVERT: A 599 ASN cc_start: 0.7401 (p0) cc_final: 0.6954 (p0) outliers start: 21 outliers final: 16 residues processed: 86 average time/residue: 0.2839 time to fit residues: 25.8532 Evaluate side-chains 87 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 567 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 52 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.121886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.105201 restraints weight = 6460.299| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.98 r_work: 0.3125 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4674 Z= 0.142 Angle : 0.560 8.809 6389 Z= 0.274 Chirality : 0.040 0.188 703 Planarity : 0.004 0.035 765 Dihedral : 6.757 50.017 812 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 4.02 % Allowed : 23.47 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.36), residues: 549 helix: 1.83 (0.27), residues: 381 sheet: None (None), residues: 0 loop : -0.87 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 575 TYR 0.017 0.001 TYR A 69 PHE 0.015 0.002 PHE A 458 TRP 0.011 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 4673) covalent geometry : angle 0.56019 / 0.27 ( 6387) SS BOND : bond 0.00060 / 0.04 ( 1) SS BOND : angle 0.65967 / 0.44 ( 2) hydrogen bonds : bond 0.03997 / 2.67 ( 281) hydrogen bonds : angle 4.54762 / 3.44 ( 834) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: A 53 SER cc_start: 0.8270 (m) cc_final: 0.7694 (p) REVERT: A 286 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7206 (mm-30) REVERT: A 428 ARG cc_start: 0.7394 (ttt-90) cc_final: 0.6170 (ptp-110) REVERT: A 460 TYR cc_start: 0.8531 (t80) cc_final: 0.8139 (t80) REVERT: A 599 ASN cc_start: 0.7460 (p0) cc_final: 0.7036 (p0) outliers start: 19 outliers final: 14 residues processed: 88 average time/residue: 0.2946 time to fit residues: 27.5845 Evaluate side-chains 87 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 565 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 13 optimal weight: 0.0870 chunk 31 optimal weight: 0.8980 chunk 23 optimal weight: 0.0020 chunk 28 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 overall best weight: 0.4766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.123809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.107065 restraints weight = 6481.532| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.00 r_work: 0.3152 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4674 Z= 0.115 Angle : 0.541 9.272 6389 Z= 0.262 Chirality : 0.039 0.191 703 Planarity : 0.004 0.035 765 Dihedral : 6.574 50.752 812 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.17 % Allowed : 25.37 % Favored : 71.46 % 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: 1.63 (0.36), residues: 549 helix: 1.87 (0.27), residues: 383 sheet: None (None), residues: 0 loop : -0.81 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 575 TYR 0.018 0.001 TYR A 426 PHE 0.019 0.001 PHE A 458 TRP 0.014 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 4673) covalent geometry : angle 0.54073 / 0.26 ( 6387) SS BOND : bond 0.00066 / 0.04 ( 1) SS BOND : angle 0.51223 / 0.31 ( 2) hydrogen bonds : bond 0.03727 / 2.47 ( 281) hydrogen bonds : angle 4.48196 / 3.38 ( 834) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 53 SER cc_start: 0.8181 (m) cc_final: 0.7665 (p) REVERT: A 286 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7186 (mm-30) REVERT: A 428 ARG cc_start: 0.7410 (ttt-90) cc_final: 0.6177 (ptp-110) REVERT: A 460 TYR cc_start: 0.8565 (t80) cc_final: 0.8075 (t80) REVERT: A 599 ASN cc_start: 0.7455 (p0) cc_final: 0.7022 (p0) outliers start: 15 outliers final: 12 residues processed: 84 average time/residue: 0.3663 time to fit residues: 32.7712 Evaluate side-chains 85 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 586 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 23 optimal weight: 0.0670 chunk 44 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.123168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.106584 restraints weight = 6350.013| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.98 r_work: 0.3142 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4674 Z= 0.126 Angle : 0.556 9.608 6389 Z= 0.269 Chirality : 0.040 0.187 703 Planarity : 0.004 0.035 765 Dihedral : 6.532 50.763 812 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.02 % Allowed : 24.52 % Favored : 71.46 % 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: 1.62 (0.36), residues: 549 helix: 1.87 (0.27), residues: 382 sheet: None (None), residues: 0 loop : -0.82 (0.46), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 575 TYR 0.015 0.001 TYR A 138 PHE 0.023 0.001 PHE A 458 TRP 0.012 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 4673) covalent geometry : angle 0.55595 / 0.27 ( 6387) SS BOND : bond 0.00048 / 0.03 ( 1) SS BOND : angle 0.53207 / 0.34 ( 2) hydrogen bonds : bond 0.03813 / 2.54 ( 281) hydrogen bonds : angle 4.49814 / 3.39 ( 834) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.128 Fit side-chains revert: symmetry clash REVERT: A 53 SER cc_start: 0.8182 (m) cc_final: 0.7709 (p) REVERT: A 286 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7195 (mm-30) REVERT: A 428 ARG cc_start: 0.7412 (ttt-90) cc_final: 0.6180 (ptp-110) REVERT: A 460 TYR cc_start: 0.8547 (t80) cc_final: 0.8108 (t80) REVERT: A 599 ASN cc_start: 0.7485 (p0) cc_final: 0.7063 (p0) outliers start: 19 outliers final: 13 residues processed: 84 average time/residue: 0.3218 time to fit residues: 28.7268 Evaluate side-chains 86 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 586 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.122443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.105877 restraints weight = 6413.194| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.98 r_work: 0.3134 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4674 Z= 0.135 Angle : 0.564 9.451 6389 Z= 0.274 Chirality : 0.040 0.188 703 Planarity : 0.004 0.035 765 Dihedral : 6.528 51.123 812 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.96 % Allowed : 26.22 % Favored : 70.82 % 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: 1.56 (0.36), residues: 549 helix: 1.83 (0.27), residues: 382 sheet: None (None), residues: 0 loop : -0.84 (0.46), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 575 TYR 0.016 0.001 TYR A 69 PHE 0.023 0.001 PHE A 458 TRP 0.012 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 4673) covalent geometry : angle 0.56366 / 0.27 ( 6387) SS BOND : bond 0.00060 / 0.04 ( 1) SS BOND : angle 0.56186 / 0.37 ( 2) hydrogen bonds : bond 0.03902 / 2.60 ( 281) hydrogen bonds : angle 4.52369 / 3.41 ( 834) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: A 49 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7436 (m-30) REVERT: A 53 SER cc_start: 0.8209 (m) cc_final: 0.7686 (p) REVERT: A 286 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7188 (mm-30) REVERT: A 428 ARG cc_start: 0.7344 (ttt-90) cc_final: 0.6114 (ptp-110) REVERT: A 460 TYR cc_start: 0.8568 (t80) cc_final: 0.8209 (t80) REVERT: A 599 ASN cc_start: 0.7458 (p0) cc_final: 0.7041 (p0) outliers start: 14 outliers final: 11 residues processed: 81 average time/residue: 0.2735 time to fit residues: 23.4891 Evaluate side-chains 85 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 565 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 13 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 0.0270 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 39 optimal weight: 0.0370 chunk 42 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.124508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.107905 restraints weight = 6434.432| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.99 r_work: 0.3158 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4674 Z= 0.110 Angle : 0.531 5.917 6389 Z= 0.260 Chirality : 0.039 0.191 703 Planarity : 0.004 0.035 765 Dihedral : 6.392 51.633 812 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.75 % Allowed : 26.22 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.36), residues: 549 helix: 1.90 (0.27), residues: 383 sheet: None (None), residues: 0 loop : -0.82 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 177 TYR 0.014 0.001 TYR A 138 PHE 0.019 0.001 PHE A 458 TRP 0.014 0.001 TRP A 470 HIS 0.002 0.000 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 4673) covalent geometry : angle 0.53101 / 0.26 ( 6387) SS BOND : bond 0.00055 / 0.04 ( 1) SS BOND : angle 0.44073 / 0.26 ( 2) hydrogen bonds : bond 0.03671 / 2.43 ( 281) hydrogen bonds : angle 4.48188 / 3.37 ( 834) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1415.86 seconds wall clock time: 24 minutes 56.46 seconds (1496.46 seconds total)