Starting phenix.real_space_refine on Fri Aug 22 14:02:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u55_63862/08_2025/9u55_63862.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u55_63862/08_2025/9u55_63862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9u55_63862/08_2025/9u55_63862.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u55_63862/08_2025/9u55_63862.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9u55_63862/08_2025/9u55_63862.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u55_63862/08_2025/9u55_63862.map" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 2416 2.51 5 N 619 2.21 5 O 643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3707 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3688 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 26, 'TRANS': 469} Chain breaks: 3 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 8, 'ASP:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 7, 'GLN:plan1': 6, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 108 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'RTO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.26, per 1000 atoms: 0.34 Number of scatterers: 3707 At special positions: 0 Unit cell: (101.588, 53.124, 68.968, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 29 16.00 O 643 8.00 N 619 7.00 C 2416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 105 " distance=2.01 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 128 " 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: 0.25 Conformation dependent library (CDL) restraints added in 127.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 918 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 1 sheets defined 79.8% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 removed outlier: 3.652A pdb=" N LEU A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 9 " --> pdb=" O ASP A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 26 Processing helix chain 'A' and resid 27 through 29 No H-bonds generated for 'chain 'A' and resid 27 through 29' Processing helix chain 'A' and resid 30 through 36 Processing helix chain 'A' and resid 37 through 40 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'A' and resid 131 through 160 removed outlier: 4.325A pdb=" N GLN A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 181 Processing helix chain 'A' and resid 184 through 213 removed outlier: 3.621A pdb=" N MET A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 219 Processing helix chain 'A' and resid 220 through 244 removed outlier: 3.511A pdb=" N GLY A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY A 233 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 Processing helix chain 'A' and resid 256 through 265 removed outlier: 4.067A pdb=" N ALA A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 271 through 279 Processing helix chain 'A' and resid 280 through 296 Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 305 through 312 removed outlier: 3.535A pdb=" N ALA A 311 " --> pdb=" O GLU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 332 removed outlier: 4.136A pdb=" N LEU A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 359 removed outlier: 3.583A pdb=" N LEU A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 392 removed outlier: 3.968A pdb=" N ASP A 378 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU A 379 " --> pdb=" O GLY A 375 " (cutoff:3.500A) Proline residue: A 380 - end of helix removed outlier: 3.554A pdb=" N LEU A 383 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 415 removed outlier: 3.700A pdb=" N ALA A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 449 removed outlier: 3.575A pdb=" N ARG A 423 " --> pdb=" O GLN A 419 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 452 No H-bonds generated for 'chain 'A' and resid 450 through 452' Processing helix chain 'A' and resid 453 through 477 Proline residue: A 473 - end of helix Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'A' and resid 484 through 501 Proline residue: A 494 - end of helix Processing helix chain 'A' and resid 515 through 522 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 259 hydrogen bonds defined for protein. 768 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: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 571 1.31 - 1.44: 1036 1.44 - 1.56: 2143 1.56 - 1.68: 1 1.68 - 1.81: 45 Bond restraints: 3796 Sorted by residual: bond pdb=" N04 RTO A 601 " pdb=" S08 RTO A 601 " ideal model delta sigma weight residual 1.625 1.742 -0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" C CYS A 128 " pdb=" O CYS A 128 " ideal model delta sigma weight residual 1.243 1.205 0.038 9.50e-03 1.11e+04 1.61e+01 bond pdb=" C SER A 472 " pdb=" O SER A 472 " ideal model delta sigma weight residual 1.244 1.204 0.040 1.00e-02 1.00e+04 1.57e+01 bond pdb=" C THR A 424 " pdb=" O THR A 424 " ideal model delta sigma weight residual 1.237 1.192 0.045 1.16e-02 7.43e+03 1.51e+01 bond pdb=" C PHE A 339 " pdb=" O PHE A 339 " ideal model delta sigma weight residual 1.236 1.193 0.044 1.15e-02 7.56e+03 1.44e+01 ... (remaining 3791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 4927 2.86 - 5.73: 228 5.73 - 8.59: 30 8.59 - 11.45: 2 11.45 - 14.31: 1 Bond angle restraints: 5188 Sorted by residual: angle pdb=" N SER A 77 " pdb=" CA SER A 77 " pdb=" C SER A 77 " ideal model delta sigma weight residual 111.36 118.90 -7.54 1.09e+00 8.42e-01 4.78e+01 angle pdb=" C MET A 358 " pdb=" CA MET A 358 " pdb=" CB MET A 358 " ideal model delta sigma weight residual 109.99 124.30 -14.31 2.09e+00 2.29e-01 4.69e+01 angle pdb=" N ASN A 412 " pdb=" CA ASN A 412 " pdb=" C ASN A 412 " ideal model delta sigma weight residual 111.69 103.39 8.30 1.23e+00 6.61e-01 4.55e+01 angle pdb=" N PHE A 259 " pdb=" CA PHE A 259 " pdb=" C PHE A 259 " ideal model delta sigma weight residual 112.90 105.02 7.88 1.31e+00 5.83e-01 3.62e+01 angle pdb=" N VAL A 143 " pdb=" CA VAL A 143 " pdb=" C VAL A 143 " ideal model delta sigma weight residual 110.62 104.53 6.09 1.02e+00 9.61e-01 3.57e+01 ... (remaining 5183 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 2071 17.59 - 35.18: 126 35.18 - 52.76: 26 52.76 - 70.35: 5 70.35 - 87.94: 3 Dihedral angle restraints: 2231 sinusoidal: 806 harmonic: 1425 Sorted by residual: dihedral pdb=" C MET A 358 " pdb=" N MET A 358 " pdb=" CA MET A 358 " pdb=" CB MET A 358 " ideal model delta harmonic sigma weight residual -122.60 -144.62 22.02 0 2.50e+00 1.60e-01 7.76e+01 dihedral pdb=" N MET A 358 " pdb=" C MET A 358 " pdb=" CA MET A 358 " pdb=" CB MET A 358 " ideal model delta harmonic sigma weight residual 122.80 139.31 -16.51 0 2.50e+00 1.60e-01 4.36e+01 dihedral pdb=" C VAL A 164 " pdb=" N VAL A 164 " pdb=" CA VAL A 164 " pdb=" CB VAL A 164 " ideal model delta harmonic sigma weight residual -122.00 -131.52 9.52 0 2.50e+00 1.60e-01 1.45e+01 ... (remaining 2228 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.162: 572 0.162 - 0.323: 43 0.323 - 0.485: 1 0.485 - 0.646: 0 0.646 - 0.807: 1 Chirality restraints: 617 Sorted by residual: chirality pdb=" CA MET A 358 " pdb=" N MET A 358 " pdb=" C MET A 358 " pdb=" CB MET A 358 " both_signs ideal model delta sigma weight residual False 2.51 1.70 0.81 2.00e-01 2.50e+01 1.63e+01 chirality pdb=" CA PHE A 152 " pdb=" N PHE A 152 " pdb=" C PHE A 152 " pdb=" CB PHE A 152 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CA TYR A 354 " pdb=" N TYR A 354 " pdb=" C TYR A 354 " pdb=" CB TYR A 354 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 614 not shown) Planarity restraints: 648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 493 " -0.039 5.00e-02 4.00e+02 5.87e-02 5.52e+00 pdb=" N PRO A 494 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 494 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 494 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 499 " -0.012 2.00e-02 2.50e+03 2.30e-02 5.28e+00 pdb=" C ALA A 499 " 0.040 2.00e-02 2.50e+03 pdb=" O ALA A 499 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL A 500 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 255 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.67e+00 pdb=" C SER A 255 " -0.037 2.00e-02 2.50e+03 pdb=" O SER A 255 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA A 256 " 0.013 2.00e-02 2.50e+03 ... (remaining 645 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.86: 1284 2.86 - 3.37: 3862 3.37 - 3.88: 6460 3.88 - 4.39: 7688 4.39 - 4.90: 12292 Nonbonded interactions: 31586 Sorted by model distance: nonbonded pdb=" ND2 ASN A 39 " pdb=" O MET A 358 " model vdw 2.344 3.120 nonbonded pdb=" N HIS A 48 " pdb=" O HIS A 48 " model vdw 2.402 2.496 nonbonded pdb=" N THR A 119 " pdb=" O THR A 119 " model vdw 2.407 2.496 nonbonded pdb=" O SER A 472 " pdb=" OH TYR A 490 " model vdw 2.488 3.040 nonbonded pdb=" O THR A 224 " pdb=" C LEU A 225 " model vdw 2.514 3.270 ... (remaining 31581 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.610 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 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 : 0.011 0.117 3798 Z= 0.788 Angle : 1.381 14.314 5192 Z= 0.928 Chirality : 0.089 0.807 617 Planarity : 0.007 0.059 648 Dihedral : 12.435 87.935 1307 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.53 % Allowed : 3.46 % Favored : 96.01 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.36), residues: 488 helix: -0.76 (0.25), residues: 368 sheet: -0.13 (1.48), residues: 10 loop : 0.18 (0.60), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 394 TYR 0.024 0.003 TYR A 264 PHE 0.019 0.003 PHE A 351 TRP 0.017 0.002 TRP A 346 HIS 0.007 0.002 HIS A 246 Details of bonding type rmsd covalent geometry : bond 0.01056 ( 3796) covalent geometry : angle 1.38084 ( 5188) SS BOND : bond 0.01657 ( 2) SS BOND : angle 1.42413 ( 4) hydrogen bonds : bond 0.21992 ( 259) hydrogen bonds : angle 7.95602 ( 768) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 140 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8346 (t0) cc_final: 0.8104 (t0) REVERT: A 214 MET cc_start: 0.7520 (mtp) cc_final: 0.6953 (ttm) REVERT: A 387 LEU cc_start: 0.8186 (mt) cc_final: 0.7788 (mt) outliers start: 2 outliers final: 0 residues processed: 141 average time/residue: 0.0683 time to fit residues: 11.9256 Evaluate side-chains 96 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 39 ASN A 205 ASN A 217 HIS A 246 HIS A 439 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.161981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.131226 restraints weight = 5180.278| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.18 r_work: 0.3509 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3798 Z= 0.168 Angle : 0.652 7.589 5192 Z= 0.334 Chirality : 0.041 0.166 617 Planarity : 0.006 0.035 648 Dihedral : 4.862 42.183 549 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.66 % Allowed : 9.31 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.38), residues: 488 helix: 0.92 (0.27), residues: 371 sheet: -0.68 (1.56), residues: 10 loop : 1.08 (0.65), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 219 TYR 0.012 0.002 TYR A 444 PHE 0.017 0.002 PHE A 351 TRP 0.011 0.001 TRP A 346 HIS 0.011 0.002 HIS A 217 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 3796) covalent geometry : angle 0.65163 ( 5188) SS BOND : bond 0.00627 ( 2) SS BOND : angle 0.58775 ( 4) hydrogen bonds : bond 0.05257 ( 259) hydrogen bonds : angle 4.57844 ( 768) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: A 154 TYR cc_start: 0.8545 (t80) cc_final: 0.8246 (t80) REVERT: A 447 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7430 (mt-10) outliers start: 10 outliers final: 7 residues processed: 100 average time/residue: 0.0479 time to fit residues: 6.2450 Evaluate side-chains 87 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.0980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 39 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.157804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.127110 restraints weight = 5130.609| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.16 r_work: 0.3454 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3798 Z= 0.137 Angle : 0.580 7.491 5192 Z= 0.291 Chirality : 0.039 0.155 617 Planarity : 0.004 0.030 648 Dihedral : 4.240 25.150 549 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.66 % Allowed : 12.50 % Favored : 84.84 % 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 aren not related in a simple way. whole: 2.08 (0.39), residues: 488 helix: 1.58 (0.27), residues: 368 sheet: -0.95 (1.77), residues: 10 loop : 1.25 (0.68), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 423 TYR 0.008 0.001 TYR A 444 PHE 0.014 0.001 PHE A 351 TRP 0.009 0.001 TRP A 274 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 3796) covalent geometry : angle 0.58052 ( 5188) SS BOND : bond 0.00482 ( 2) SS BOND : angle 0.44921 ( 4) hydrogen bonds : bond 0.04688 ( 259) hydrogen bonds : angle 4.19441 ( 768) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.140 Fit side-chains REVERT: A 85 GLN cc_start: 0.8126 (mm110) cc_final: 0.7846 (mm110) REVERT: A 112 ASP cc_start: 0.8202 (t0) cc_final: 0.8001 (t0) REVERT: A 154 TYR cc_start: 0.8535 (t80) cc_final: 0.8329 (t80) REVERT: A 204 LEU cc_start: 0.8612 (tp) cc_final: 0.8396 (mp) outliers start: 10 outliers final: 6 residues processed: 99 average time/residue: 0.0507 time to fit residues: 6.6463 Evaluate side-chains 89 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 458 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 9 optimal weight: 0.0670 chunk 32 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.153517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.123127 restraints weight = 5108.417| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.13 r_work: 0.3410 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3798 Z= 0.137 Angle : 0.576 8.027 5192 Z= 0.283 Chirality : 0.039 0.216 617 Planarity : 0.004 0.024 648 Dihedral : 4.206 24.499 549 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.39 % Allowed : 13.56 % Favored : 84.04 % 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 aren not related in a simple way. whole: 2.29 (0.39), residues: 488 helix: 1.75 (0.27), residues: 369 sheet: -1.20 (1.86), residues: 10 loop : 1.27 (0.69), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 219 TYR 0.011 0.001 TYR A 264 PHE 0.017 0.001 PHE A 351 TRP 0.008 0.001 TRP A 247 HIS 0.003 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 3796) covalent geometry : angle 0.57571 ( 5188) SS BOND : bond 0.00436 ( 2) SS BOND : angle 0.38183 ( 4) hydrogen bonds : bond 0.04510 ( 259) hydrogen bonds : angle 4.03317 ( 768) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.144 Fit side-chains REVERT: A 18 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7866 (mp10) REVERT: A 85 GLN cc_start: 0.8003 (mm110) cc_final: 0.7758 (mm110) REVERT: A 112 ASP cc_start: 0.8235 (t0) cc_final: 0.8003 (t0) REVERT: A 154 TYR cc_start: 0.8554 (t80) cc_final: 0.8343 (t80) REVERT: A 447 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7865 (mt-10) outliers start: 9 outliers final: 8 residues processed: 93 average time/residue: 0.0550 time to fit residues: 6.7051 Evaluate side-chains 89 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 458 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.145641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.115649 restraints weight = 5253.409| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.15 r_work: 0.3324 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3798 Z= 0.171 Angle : 0.602 7.860 5192 Z= 0.300 Chirality : 0.040 0.207 617 Planarity : 0.004 0.024 648 Dihedral : 4.324 22.717 549 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.66 % Allowed : 14.63 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.40), residues: 488 helix: 1.73 (0.28), residues: 368 sheet: -1.14 (1.97), residues: 10 loop : 0.97 (0.67), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 395 TYR 0.012 0.002 TYR A 354 PHE 0.022 0.002 PHE A 3 TRP 0.009 0.001 TRP A 274 HIS 0.003 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 3796) covalent geometry : angle 0.60238 ( 5188) SS BOND : bond 0.00575 ( 2) SS BOND : angle 0.39401 ( 4) hydrogen bonds : bond 0.04889 ( 259) hydrogen bonds : angle 4.05045 ( 768) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.135 Fit side-chains REVERT: A 112 ASP cc_start: 0.8272 (t0) cc_final: 0.8033 (t0) REVERT: A 447 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8142 (mt-10) outliers start: 10 outliers final: 6 residues processed: 95 average time/residue: 0.0476 time to fit residues: 6.1120 Evaluate side-chains 88 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 3 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 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 = 0.3859 r_free = 0.3859 target = 0.147462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.119385 restraints weight = 5186.317| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.03 r_work: 0.3353 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3798 Z= 0.139 Angle : 0.580 7.332 5192 Z= 0.286 Chirality : 0.040 0.224 617 Planarity : 0.004 0.031 648 Dihedral : 4.265 22.263 549 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.13 % Allowed : 16.22 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.39), residues: 488 helix: 1.84 (0.27), residues: 366 sheet: -1.23 (2.07), residues: 10 loop : 0.90 (0.65), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 395 TYR 0.010 0.001 TYR A 264 PHE 0.017 0.001 PHE A 351 TRP 0.009 0.001 TRP A 247 HIS 0.003 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 3796) covalent geometry : angle 0.57966 ( 5188) SS BOND : bond 0.00420 ( 2) SS BOND : angle 0.36327 ( 4) hydrogen bonds : bond 0.04518 ( 259) hydrogen bonds : angle 3.94237 ( 768) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.151 Fit side-chains REVERT: A 107 ASP cc_start: 0.8246 (m-30) cc_final: 0.8014 (m-30) REVERT: A 112 ASP cc_start: 0.8278 (t0) cc_final: 0.8006 (t0) REVERT: A 134 ARG cc_start: 0.8935 (ttp80) cc_final: 0.8586 (ttt90) REVERT: A 447 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8096 (mt-10) outliers start: 8 outliers final: 8 residues processed: 96 average time/residue: 0.0532 time to fit residues: 6.7376 Evaluate side-chains 90 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 25 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 41 optimal weight: 0.0980 chunk 8 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.145670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.116132 restraints weight = 5323.493| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.15 r_work: 0.3333 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3798 Z= 0.144 Angle : 0.602 8.485 5192 Z= 0.294 Chirality : 0.040 0.251 617 Planarity : 0.004 0.035 648 Dihedral : 4.309 26.938 549 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 3.19 % Allowed : 16.49 % Favored : 80.32 % 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 aren not related in a simple way. whole: 2.47 (0.40), residues: 488 helix: 1.99 (0.28), residues: 366 sheet: -1.51 (1.91), residues: 10 loop : 0.96 (0.65), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 219 TYR 0.011 0.001 TYR A 354 PHE 0.017 0.001 PHE A 351 TRP 0.009 0.001 TRP A 247 HIS 0.003 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 3796) covalent geometry : angle 0.60212 ( 5188) SS BOND : bond 0.00469 ( 2) SS BOND : angle 0.30987 ( 4) hydrogen bonds : bond 0.04526 ( 259) hydrogen bonds : angle 3.90260 ( 768) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.150 Fit side-chains REVERT: A 107 ASP cc_start: 0.8170 (m-30) cc_final: 0.7959 (m-30) REVERT: A 112 ASP cc_start: 0.8263 (t0) cc_final: 0.7994 (t0) REVERT: A 205 ASN cc_start: 0.8557 (m-40) cc_final: 0.8315 (m110) REVERT: A 344 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7096 (mpp) REVERT: A 447 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8113 (mt-10) outliers start: 12 outliers final: 10 residues processed: 91 average time/residue: 0.0537 time to fit residues: 6.4528 Evaluate side-chains 89 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 29 optimal weight: 0.0050 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.147102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.119281 restraints weight = 5189.968| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.04 r_work: 0.3373 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3798 Z= 0.128 Angle : 0.581 8.679 5192 Z= 0.282 Chirality : 0.039 0.243 617 Planarity : 0.004 0.038 648 Dihedral : 4.231 25.294 549 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.66 % Allowed : 17.55 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.51 (0.40), residues: 488 helix: 1.99 (0.28), residues: 372 sheet: -1.23 (1.98), residues: 10 loop : 1.00 (0.66), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 219 TYR 0.018 0.002 TYR A 264 PHE 0.017 0.001 PHE A 351 TRP 0.008 0.001 TRP A 247 HIS 0.002 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 3796) covalent geometry : angle 0.58076 ( 5188) SS BOND : bond 0.00361 ( 2) SS BOND : angle 0.33972 ( 4) hydrogen bonds : bond 0.04322 ( 259) hydrogen bonds : angle 3.84520 ( 768) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.147 Fit side-chains REVERT: A 112 ASP cc_start: 0.8235 (t0) cc_final: 0.7961 (t0) REVERT: A 205 ASN cc_start: 0.8552 (m-40) cc_final: 0.8326 (m110) REVERT: A 344 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7127 (mpp) REVERT: A 447 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8114 (mt-10) outliers start: 10 outliers final: 9 residues processed: 87 average time/residue: 0.0474 time to fit residues: 5.5571 Evaluate side-chains 87 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 45 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 46 optimal weight: 0.4980 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.145190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.115728 restraints weight = 5241.843| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.14 r_work: 0.3334 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.5513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3798 Z= 0.143 Angle : 0.607 8.755 5192 Z= 0.299 Chirality : 0.040 0.226 617 Planarity : 0.004 0.039 648 Dihedral : 4.269 25.305 549 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.19 % Allowed : 17.82 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.35 (0.40), residues: 488 helix: 1.87 (0.28), residues: 372 sheet: -1.25 (1.94), residues: 10 loop : 0.96 (0.65), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 395 TYR 0.012 0.001 TYR A 154 PHE 0.017 0.001 PHE A 351 TRP 0.009 0.001 TRP A 247 HIS 0.003 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 3796) covalent geometry : angle 0.60703 ( 5188) SS BOND : bond 0.00402 ( 2) SS BOND : angle 0.27541 ( 4) hydrogen bonds : bond 0.04469 ( 259) hydrogen bonds : angle 3.83466 ( 768) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.142 Fit side-chains REVERT: A 112 ASP cc_start: 0.8232 (t0) cc_final: 0.7979 (t0) REVERT: A 344 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7139 (mpp) REVERT: A 447 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8098 (mt-10) outliers start: 12 outliers final: 10 residues processed: 84 average time/residue: 0.0498 time to fit residues: 5.6102 Evaluate side-chains 88 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 48 optimal weight: 0.3980 chunk 23 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 0 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 205 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.147679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.119835 restraints weight = 5256.385| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.07 r_work: 0.3373 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.5629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3798 Z= 0.125 Angle : 0.575 8.932 5192 Z= 0.279 Chirality : 0.039 0.226 617 Planarity : 0.004 0.039 648 Dihedral : 4.198 24.796 549 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.93 % Allowed : 17.29 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.40), residues: 488 helix: 1.94 (0.28), residues: 372 sheet: -1.30 (1.92), residues: 10 loop : 0.96 (0.65), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 219 TYR 0.012 0.001 TYR A 154 PHE 0.017 0.001 PHE A 351 TRP 0.009 0.001 TRP A 274 HIS 0.003 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 3796) covalent geometry : angle 0.57494 ( 5188) SS BOND : bond 0.00327 ( 2) SS BOND : angle 0.30351 ( 4) hydrogen bonds : bond 0.04242 ( 259) hydrogen bonds : angle 3.77876 ( 768) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.169 Fit side-chains REVERT: A 112 ASP cc_start: 0.8220 (t0) cc_final: 0.7955 (t0) REVERT: A 344 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.6963 (mpp) outliers start: 11 outliers final: 9 residues processed: 89 average time/residue: 0.0560 time to fit residues: 6.5736 Evaluate side-chains 86 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 0 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.1980 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.144235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.116102 restraints weight = 5151.450| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.07 r_work: 0.3333 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.5719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3798 Z= 0.149 Angle : 0.605 8.978 5192 Z= 0.296 Chirality : 0.041 0.215 617 Planarity : 0.004 0.040 648 Dihedral : 4.292 24.942 549 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.93 % Allowed : 18.35 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.36 (0.40), residues: 488 helix: 1.88 (0.28), residues: 372 sheet: -1.65 (1.82), residues: 10 loop : 0.99 (0.66), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 395 TYR 0.012 0.001 TYR A 154 PHE 0.017 0.001 PHE A 351 TRP 0.009 0.001 TRP A 247 HIS 0.003 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 3796) covalent geometry : angle 0.60515 ( 5188) SS BOND : bond 0.00424 ( 2) SS BOND : angle 0.30024 ( 4) hydrogen bonds : bond 0.04462 ( 259) hydrogen bonds : angle 3.84542 ( 768) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1168.57 seconds wall clock time: 20 minutes 43.16 seconds (1243.16 seconds total)