Starting phenix.real_space_refine on Wed Jul 1 23:52:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y7z_33675/07_2026/7y7z_33675.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y7z_33675/07_2026/7y7z_33675.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7y7z_33675/07_2026/7y7z_33675.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y7z_33675/07_2026/7y7z_33675.cif" model { file = "/net/cci-nas-00/data/ceres_data/7y7z_33675/07_2026/7y7z_33675.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y7z_33675/07_2026/7y7z_33675.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y7z_33675/07_2026/7y7z_33675.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y7z_33675/07_2026/7y7z_33675.map" } resolution = 3.2 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= 0.130 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 36 5.16 5 Cl 1 4.86 5 C 2876 2.51 5 N 661 2.21 5 O 729 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 4303 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4235 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 23, 'TRANS': 508} Chain: "A" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 68 Unusual residues: {' CL': 1, 'NAG': 3, 'TGI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 0.98, per 1000 atoms: 0.23 Number of scatterers: 4303 At special positions: 0 Unit cell: (71.445, 74.6925, 96.3425, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 36 16.00 O 729 8.00 N 661 7.00 C 2876 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 173 " distance=2.02 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 Links applied NAG-ASN " NAG A 702 " - " ASN A 181 " " NAG A 703 " - " ASN A 176 " " NAG A 704 " - " ASN A 184 " Time building additional restraints: 0.24 Conformation dependent library (CDL) restraints added in 95.9 milliseconds 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 2 sheets defined 77.4% alpha, 0.8% 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 49 through 60 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.643A pdb=" N VAL A 67 " --> pdb=" O GLY A 63 " (cutoff:3.500A) Proline residue: A 71 - end of helix Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 94 through 109 Processing helix chain 'A' and resid 119 through 122 Processing helix chain 'A' and resid 123 through 155 removed outlier: 3.764A pdb=" N LEU A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'A' and resid 211 through 230 Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.946A pdb=" N GLY A 237 " --> pdb=" O GLY A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 260 removed outlier: 3.895A pdb=" N THR A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 273 removed outlier: 3.660A pdb=" N GLY A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 296 removed outlier: 3.901A pdb=" N TRP A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 310 removed outlier: 4.157A pdb=" N ALA A 305 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 350 removed outlier: 3.518A pdb=" N GLY A 343 " --> pdb=" O PHE A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 363 through 374 removed outlier: 3.511A pdb=" N TYR A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) Proline residue: A 369 - end of helix Processing helix chain 'A' and resid 377 through 412 removed outlier: 3.668A pdb=" N TRP A 381 " --> pdb=" O ILE A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 417 Processing helix chain 'A' and resid 419 through 439 Processing helix chain 'A' and resid 442 through 454 removed outlier: 4.315A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 474 removed outlier: 3.676A pdb=" N PHE A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 489 Processing helix chain 'A' and resid 493 through 519 removed outlier: 4.511A pdb=" N LYS A 497 " --> pdb=" O CYS A 493 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N THR A 504 " --> pdb=" O TRP A 500 " (cutoff:3.500A) Proline residue: A 505 - end of helix removed outlier: 3.527A pdb=" N GLN A 518 " --> pdb=" O PHE A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 546 Processing helix chain 'A' and resid 546 through 559 removed outlier: 3.749A pdb=" N LEU A 559 " --> pdb=" O MET A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 572 Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 174 removed outlier: 3.565A pdb=" N PHE A 174 " --> pdb=" O THR A 186 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 523 through 524 282 hydrogen bonds defined for protein. 837 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: 0.56 Time building geometry restraints manager: 0.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 648 1.32 - 1.45: 1359 1.45 - 1.57: 2375 1.57 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 4440 Sorted by residual: bond pdb=" C17 TGI A 701 " pdb=" O19 TGI A 701 " ideal model delta sigma weight residual 1.261 1.203 0.058 2.00e-02 2.50e+03 8.37e+00 bond pdb=" C20 TGI A 701 " pdb=" C21 TGI A 701 " ideal model delta sigma weight residual 1.374 1.430 -0.056 2.00e-02 2.50e+03 7.91e+00 bond pdb=" C17 TGI A 701 " pdb=" O18 TGI A 701 " ideal model delta sigma weight residual 1.260 1.204 0.056 2.00e-02 2.50e+03 7.80e+00 bond pdb=" N VAL A 323 " pdb=" CA VAL A 323 " ideal model delta sigma weight residual 1.461 1.492 -0.030 1.17e-02 7.31e+03 6.73e+00 bond pdb=" C02 TGI A 701 " pdb=" C03 TGI A 701 " ideal model delta sigma weight residual 1.380 1.423 -0.043 2.00e-02 2.50e+03 4.57e+00 ... (remaining 4435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 5561 1.15 - 2.30: 382 2.30 - 3.45: 71 3.45 - 4.59: 27 4.59 - 5.74: 8 Bond angle restraints: 6049 Sorted by residual: angle pdb=" CA TYR A 60 " pdb=" CB TYR A 60 " pdb=" CG TYR A 60 " ideal model delta sigma weight residual 113.90 119.64 -5.74 1.80e+00 3.09e-01 1.02e+01 angle pdb=" C ILE A 138 " pdb=" N TYR A 139 " pdb=" CA TYR A 139 " ideal model delta sigma weight residual 121.14 115.83 5.31 1.75e+00 3.27e-01 9.22e+00 angle pdb=" CA VAL A 323 " pdb=" C VAL A 323 " pdb=" O VAL A 323 " ideal model delta sigma weight residual 121.17 118.28 2.89 1.06e+00 8.90e-01 7.43e+00 angle pdb=" O VAL A 323 " pdb=" C VAL A 323 " pdb=" N CYS A 324 " ideal model delta sigma weight residual 121.91 124.44 -2.53 9.80e-01 1.04e+00 6.67e+00 angle pdb=" CA TYR A 139 " pdb=" CB TYR A 139 " pdb=" CG TYR A 139 " ideal model delta sigma weight residual 113.90 118.46 -4.56 1.80e+00 3.09e-01 6.41e+00 ... (remaining 6044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.49: 2230 20.49 - 40.98: 246 40.98 - 61.47: 16 61.47 - 81.96: 2 81.96 - 102.45: 2 Dihedral angle restraints: 2496 sinusoidal: 964 harmonic: 1532 Sorted by residual: dihedral pdb=" CA SER A 456 " pdb=" C SER A 456 " pdb=" N GLY A 457 " pdb=" CA GLY A 457 " ideal model delta harmonic sigma weight residual -180.00 -157.18 -22.82 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA PHE A 339 " pdb=" C PHE A 339 " pdb=" N SER A 340 " pdb=" CA SER A 340 " ideal model delta harmonic sigma weight residual 180.00 158.37 21.63 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA TRP A 116 " pdb=" C TRP A 116 " pdb=" N LYS A 117 " pdb=" CA LYS A 117 " ideal model delta harmonic sigma weight residual 180.00 158.74 21.26 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 2493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 512 0.049 - 0.099: 129 0.099 - 0.148: 27 0.148 - 0.198: 2 0.198 - 0.247: 1 Chirality restraints: 671 Sorted by residual: chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 176 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA VAL A 323 " pdb=" N VAL A 323 " pdb=" C VAL A 323 " pdb=" CB VAL A 323 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.28e-01 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 181 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-01 2.50e+01 6.74e-01 ... (remaining 668 not shown) Planarity restraints: 736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 184 " 0.219 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" CG ASN A 184 " -0.091 2.00e-02 2.50e+03 pdb=" OD1 ASN A 184 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN A 184 " -0.483 2.00e-02 2.50e+03 pdb=" C1 NAG A 704 " 0.333 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C03 TGI A 701 " 0.009 2.00e-02 2.50e+03 1.80e-01 4.05e+02 pdb=" C07 TGI A 701 " 0.042 2.00e-02 2.50e+03 pdb=" C08 TGI A 701 " 0.307 2.00e-02 2.50e+03 pdb=" C09 TGI A 701 " -0.210 2.00e-02 2.50e+03 pdb=" C20 TGI A 701 " -0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 176 " -0.099 2.00e-02 2.50e+03 1.58e-01 3.11e+02 pdb=" CG ASN A 176 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN A 176 " -0.055 2.00e-02 2.50e+03 pdb=" ND2 ASN A 176 " 0.282 2.00e-02 2.50e+03 pdb=" C1 NAG A 703 " -0.173 2.00e-02 2.50e+03 ... (remaining 733 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 38 2.61 - 3.18: 4047 3.18 - 3.75: 6585 3.75 - 4.33: 8993 4.33 - 4.90: 15408 Nonbonded interactions: 35071 Sorted by model distance: nonbonded pdb=" OG1 THR A 170 " pdb=" OE2 GLU A 191 " model vdw 2.037 3.040 nonbonded pdb=" O GLY A 561 " pdb=" NH1 ARG A 566 " model vdw 2.119 3.120 nonbonded pdb=" O LEU A 279 " pdb=" OG SER A 280 " model vdw 2.258 3.040 nonbonded pdb=" O GLY A 114 " pdb=" N LYS A 117 " model vdw 2.278 3.120 nonbonded pdb=" OD1 ASN A 181 " pdb=" OG1 THR A 183 " model vdw 2.304 3.040 ... (remaining 35066 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: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 4.570 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 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 0.103 4444 Z= 0.295 Angle : 0.862 26.323 6060 Z= 0.421 Chirality : 0.045 0.247 671 Planarity : 0.009 0.180 733 Dihedral : 15.523 102.447 1521 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % 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: -0.11 (0.38), residues: 530 helix: 0.55 (0.27), residues: 395 sheet: None (None), residues: 0 loop : -1.79 (0.56), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 69 TYR 0.029 0.002 TYR A 60 PHE 0.016 0.002 PHE A 512 TRP 0.021 0.002 TRP A 193 HIS 0.002 0.001 HIS A 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.27 ( 4440) covalent geometry : angle 0.71185 / 0.39 ( 6049) SS BOND : bond 0.00608 / 0.38 ( 1) SS BOND : angle 2.12729 / 0.75 ( 2) hydrogen bonds : bond 0.11080 / 7.36 ( 282) hydrogen bonds : angle 5.80034 / 4.14 ( 837) link_NAG-ASN : bond 0.09780 / 5.49 ( 3) link_NAG-ASN : angle 12.61290 / 5.75 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.147 Fit side-chains REVERT: A 152 TYR cc_start: 0.8218 (t80) cc_final: 0.7910 (t80) REVERT: A 314 ASN cc_start: 0.8805 (t0) cc_final: 0.8596 (t0) REVERT: A 491 ARG cc_start: 0.8383 (mmm160) cc_final: 0.8061 (ttm170) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0659 time to fit residues: 6.2293 Evaluate side-chains 69 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 0.2980 chunk 30 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4101 r_free = 0.4101 target = 0.173079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.133388 restraints weight = 4534.952| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.94 r_work: 0.3064 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4444 Z= 0.159 Angle : 0.705 10.017 6060 Z= 0.344 Chirality : 0.047 0.329 671 Planarity : 0.005 0.040 733 Dihedral : 7.876 89.444 603 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.11 % Allowed : 9.07 % Favored : 89.82 % 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: 0.51 (0.38), residues: 530 helix: 0.97 (0.27), residues: 397 sheet: None (None), residues: 0 loop : -1.46 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 566 TYR 0.023 0.002 TYR A 60 PHE 0.017 0.002 PHE A 385 TRP 0.018 0.001 TRP A 193 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 ( 4440) covalent geometry : angle 0.68223 / 0.34 ( 6049) SS BOND : bond 0.00392 / 0.25 ( 1) SS BOND : angle 1.46004 / 0.59 ( 2) hydrogen bonds : bond 0.05665 / 3.68 ( 282) hydrogen bonds : angle 4.89828 / 3.51 ( 837) link_NAG-ASN : bond 0.00848 / 0.47 ( 3) link_NAG-ASN : angle 4.58189 / 2.19 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 314 ASN cc_start: 0.8647 (t0) cc_final: 0.8389 (t0) outliers start: 5 outliers final: 3 residues processed: 64 average time/residue: 0.0382 time to fit residues: 3.5962 Evaluate side-chains 62 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 49 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.172980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.133151 restraints weight = 4493.794| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.94 r_work: 0.3068 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4444 Z= 0.157 Angle : 0.662 9.194 6060 Z= 0.323 Chirality : 0.046 0.361 671 Planarity : 0.004 0.040 733 Dihedral : 7.626 87.172 603 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.55 % Allowed : 12.17 % Favored : 86.28 % 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: 0.78 (0.38), residues: 530 helix: 1.22 (0.27), residues: 392 sheet: None (None), residues: 0 loop : -1.47 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 566 TYR 0.026 0.002 TYR A 60 PHE 0.016 0.001 PHE A 51 TRP 0.016 0.001 TRP A 193 HIS 0.002 0.001 HIS A 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 4440) covalent geometry : angle 0.64338 / 0.32 ( 6049) SS BOND : bond 0.00215 / 0.13 ( 1) SS BOND : angle 1.53356 / 0.57 ( 2) hydrogen bonds : bond 0.05638 / 3.65 ( 282) hydrogen bonds : angle 4.78756 / 3.44 ( 837) link_NAG-ASN : bond 0.00992 / 0.55 ( 3) link_NAG-ASN : angle 3.99549 / 1.86 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.153 Fit side-chains REVERT: A 314 ASN cc_start: 0.8649 (t0) cc_final: 0.8413 (t0) outliers start: 7 outliers final: 4 residues processed: 71 average time/residue: 0.0456 time to fit residues: 4.7072 Evaluate side-chains 67 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 19 optimal weight: 0.0020 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.175814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.138056 restraints weight = 4464.233| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.14 r_work: 0.3224 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4444 Z= 0.136 Angle : 0.628 8.870 6060 Z= 0.305 Chirality : 0.045 0.363 671 Planarity : 0.004 0.043 733 Dihedral : 7.794 86.297 603 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.55 % Allowed : 14.38 % Favored : 84.07 % 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: 1.01 (0.37), residues: 530 helix: 1.36 (0.27), residues: 394 sheet: None (None), residues: 0 loop : -1.36 (0.53), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 318 TYR 0.026 0.001 TYR A 60 PHE 0.015 0.001 PHE A 474 TRP 0.015 0.001 TRP A 193 HIS 0.002 0.001 HIS A 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 ( 4440) covalent geometry : angle 0.60908 / 0.30 ( 6049) SS BOND : bond 0.00161 / 0.10 ( 1) SS BOND : angle 1.20387 / 0.43 ( 2) hydrogen bonds : bond 0.05070 / 3.30 ( 282) hydrogen bonds : angle 4.64629 / 3.34 ( 837) link_NAG-ASN : bond 0.00977 / 0.54 ( 3) link_NAG-ASN : angle 3.93669 / 1.83 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: A 314 ASN cc_start: 0.8731 (t0) cc_final: 0.8505 (t0) REVERT: A 355 ASP cc_start: 0.8272 (t0) cc_final: 0.8039 (t0) outliers start: 7 outliers final: 4 residues processed: 63 average time/residue: 0.0334 time to fit residues: 3.1699 Evaluate side-chains 57 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 chunk 51 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 27 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.172507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.132853 restraints weight = 4510.151| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.95 r_work: 0.3116 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4444 Z= 0.164 Angle : 0.638 8.841 6060 Z= 0.313 Chirality : 0.046 0.362 671 Planarity : 0.004 0.042 733 Dihedral : 7.854 83.482 603 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.99 % Allowed : 16.37 % Favored : 81.64 % 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: 0.88 (0.38), residues: 530 helix: 1.19 (0.27), residues: 409 sheet: None (None), residues: 0 loop : -1.42 (0.57), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 318 TYR 0.026 0.001 TYR A 60 PHE 0.012 0.001 PHE A 339 TRP 0.014 0.001 TRP A 193 HIS 0.001 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 ( 4440) covalent geometry : angle 0.62019 / 0.31 ( 6049) SS BOND : bond 0.00301 / 0.19 ( 1) SS BOND : angle 1.47566 / 0.51 ( 2) hydrogen bonds : bond 0.05625 / 3.64 ( 282) hydrogen bonds : angle 4.72790 / 3.41 ( 837) link_NAG-ASN : bond 0.00977 / 0.54 ( 3) link_NAG-ASN : angle 3.87210 / 1.76 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.147 Fit side-chains REVERT: A 185 MET cc_start: 0.6914 (OUTLIER) cc_final: 0.6049 (mmm) REVERT: A 314 ASN cc_start: 0.8669 (t0) cc_final: 0.8444 (t0) REVERT: A 355 ASP cc_start: 0.8375 (t0) cc_final: 0.8095 (t0) outliers start: 9 outliers final: 8 residues processed: 68 average time/residue: 0.0426 time to fit residues: 4.3084 Evaluate side-chains 69 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 34 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 18 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 32 optimal weight: 0.0050 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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 = 0.4175 r_free = 0.4175 target = 0.182806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.143397 restraints weight = 4782.215| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.46 r_work: 0.2905 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4444 Z= 0.133 Angle : 0.617 8.927 6060 Z= 0.300 Chirality : 0.044 0.374 671 Planarity : 0.004 0.044 733 Dihedral : 7.938 83.050 603 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.10 % Allowed : 16.81 % Favored : 80.09 % 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: 1.06 (0.38), residues: 530 helix: 1.31 (0.27), residues: 409 sheet: None (None), residues: 0 loop : -1.34 (0.57), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 318 TYR 0.026 0.001 TYR A 60 PHE 0.011 0.001 PHE A 51 TRP 0.019 0.001 TRP A 230 HIS 0.001 0.000 HIS A 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 4440) covalent geometry : angle 0.59960 / 0.30 ( 6049) SS BOND : bond 0.00128 / 0.08 ( 1) SS BOND : angle 1.01203 / 0.35 ( 2) hydrogen bonds : bond 0.04978 / 3.23 ( 282) hydrogen bonds : angle 4.60466 / 3.32 ( 837) link_NAG-ASN : bond 0.00996 / 0.56 ( 3) link_NAG-ASN : angle 3.83529 / 1.74 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 185 MET cc_start: 0.6915 (OUTLIER) cc_final: 0.6054 (mmm) REVERT: A 355 ASP cc_start: 0.8229 (t0) cc_final: 0.7980 (t0) outliers start: 14 outliers final: 10 residues processed: 73 average time/residue: 0.0417 time to fit residues: 4.4955 Evaluate side-chains 72 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 39 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 13 optimal weight: 8.9990 chunk 43 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4109 r_free = 0.4109 target = 0.173048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.133411 restraints weight = 4524.605| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.95 r_work: 0.3129 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4444 Z= 0.157 Angle : 0.646 9.026 6060 Z= 0.315 Chirality : 0.046 0.357 671 Planarity : 0.004 0.043 733 Dihedral : 7.959 82.376 603 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.88 % Allowed : 18.58 % Favored : 78.54 % 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: 1.06 (0.38), residues: 530 helix: 1.32 (0.26), residues: 409 sheet: None (None), residues: 0 loop : -1.32 (0.57), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 318 TYR 0.027 0.001 TYR A 60 PHE 0.012 0.001 PHE A 294 TRP 0.020 0.001 TRP A 230 HIS 0.001 0.000 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 4440) covalent geometry : angle 0.62638 / 0.31 ( 6049) SS BOND : bond 0.00280 / 0.17 ( 1) SS BOND : angle 1.41359 / 0.49 ( 2) hydrogen bonds : bond 0.05544 / 3.59 ( 282) hydrogen bonds : angle 4.66526 / 3.36 ( 837) link_NAG-ASN : bond 0.00815 / 0.45 ( 3) link_NAG-ASN : angle 4.11115 / 1.87 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: A 185 MET cc_start: 0.6890 (OUTLIER) cc_final: 0.6167 (mmm) REVERT: A 355 ASP cc_start: 0.8389 (t0) cc_final: 0.8165 (t0) REVERT: A 473 TRP cc_start: 0.8835 (m-10) cc_final: 0.8600 (m-10) outliers start: 13 outliers final: 9 residues processed: 72 average time/residue: 0.0404 time to fit residues: 4.2860 Evaluate side-chains 71 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 14 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.173884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.134124 restraints weight = 4509.810| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.95 r_work: 0.3138 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4444 Z= 0.151 Angle : 0.646 8.888 6060 Z= 0.315 Chirality : 0.046 0.377 671 Planarity : 0.004 0.045 733 Dihedral : 8.026 83.463 603 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.65 % Allowed : 18.36 % Favored : 78.98 % 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: 1.14 (0.38), residues: 530 helix: 1.36 (0.26), residues: 409 sheet: None (None), residues: 0 loop : -1.24 (0.59), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 318 TYR 0.027 0.001 TYR A 60 PHE 0.011 0.001 PHE A 339 TRP 0.020 0.001 TRP A 230 HIS 0.001 0.000 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 4440) covalent geometry : angle 0.63014 / 0.31 ( 6049) SS BOND : bond 0.00224 / 0.14 ( 1) SS BOND : angle 1.28469 / 0.45 ( 2) hydrogen bonds : bond 0.05397 / 3.49 ( 282) hydrogen bonds : angle 4.66367 / 3.35 ( 837) link_NAG-ASN : bond 0.00902 / 0.50 ( 3) link_NAG-ASN : angle 3.65911 / 1.62 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: A 179 MET cc_start: 0.5892 (tpt) cc_final: 0.5511 (mmt) REVERT: A 185 MET cc_start: 0.6764 (mtp) cc_final: 0.6311 (mmm) REVERT: A 250 MET cc_start: 0.7542 (mmm) cc_final: 0.7251 (mmm) REVERT: A 355 ASP cc_start: 0.8440 (t0) cc_final: 0.8206 (t0) REVERT: A 473 TRP cc_start: 0.8804 (m-10) cc_final: 0.8554 (m-10) outliers start: 12 outliers final: 8 residues processed: 68 average time/residue: 0.0424 time to fit residues: 4.2916 Evaluate side-chains 66 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4114 r_free = 0.4114 target = 0.173300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.133299 restraints weight = 4553.494| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.97 r_work: 0.3124 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4444 Z= 0.156 Angle : 0.645 9.101 6060 Z= 0.316 Chirality : 0.046 0.364 671 Planarity : 0.004 0.044 733 Dihedral : 8.040 83.313 603 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.43 % Allowed : 18.81 % Favored : 78.76 % 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: 1.19 (0.38), residues: 530 helix: 1.36 (0.26), residues: 410 sheet: None (None), residues: 0 loop : -1.10 (0.60), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 318 TYR 0.028 0.001 TYR A 60 PHE 0.012 0.001 PHE A 294 TRP 0.019 0.001 TRP A 230 HIS 0.001 0.000 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 4440) covalent geometry : angle 0.63118 / 0.31 ( 6049) SS BOND : bond 0.00307 / 0.19 ( 1) SS BOND : angle 1.36502 / 0.47 ( 2) hydrogen bonds : bond 0.05529 / 3.57 ( 282) hydrogen bonds : angle 4.67156 / 3.35 ( 837) link_NAG-ASN : bond 0.00741 / 0.41 ( 3) link_NAG-ASN : angle 3.49510 / 1.46 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.093 Fit side-chains revert: symmetry clash REVERT: A 179 MET cc_start: 0.5924 (tpt) cc_final: 0.5239 (mmt) REVERT: A 355 ASP cc_start: 0.8453 (t0) cc_final: 0.8222 (t0) REVERT: A 473 TRP cc_start: 0.8798 (m-10) cc_final: 0.8535 (m-10) outliers start: 11 outliers final: 10 residues processed: 71 average time/residue: 0.0361 time to fit residues: 3.7938 Evaluate side-chains 73 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.173063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.133495 restraints weight = 4499.358| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.94 r_work: 0.3127 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 4444 Z= 0.185 Angle : 1.168 52.513 6060 Z= 0.655 Chirality : 0.049 0.507 671 Planarity : 0.004 0.044 733 Dihedral : 8.077 83.472 603 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.43 % Allowed : 18.81 % Favored : 78.76 % 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: 1.21 (0.38), residues: 530 helix: 1.37 (0.26), residues: 410 sheet: None (None), residues: 0 loop : -1.08 (0.60), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 318 TYR 0.028 0.001 TYR A 60 PHE 0.011 0.001 PHE A 294 TRP 0.019 0.001 TRP A 230 HIS 0.001 0.000 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 4440) covalent geometry : angle 1.10560 / 0.64 ( 6049) SS BOND : bond 0.00272 / 0.17 ( 1) SS BOND : angle 1.34909 / 0.47 ( 2) hydrogen bonds : bond 0.05507 / 3.55 ( 282) hydrogen bonds : angle 4.66791 / 3.35 ( 837) link_NAG-ASN : bond 0.04831 / 2.68 ( 3) link_NAG-ASN : angle 9.79873 / 3.82 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: A 250 MET cc_start: 0.7573 (mmm) cc_final: 0.7315 (mmm) REVERT: A 355 ASP cc_start: 0.8448 (t0) cc_final: 0.8219 (t0) REVERT: A 473 TRP cc_start: 0.8800 (m-10) cc_final: 0.8534 (m-10) outliers start: 11 outliers final: 11 residues processed: 72 average time/residue: 0.0359 time to fit residues: 3.8488 Evaluate side-chains 74 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 546 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 39 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 31 optimal weight: 0.0970 chunk 45 optimal weight: 0.0370 chunk 6 optimal weight: 0.0070 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 overall best weight: 0.3274 ------------------------------------------------------------------------------- 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 = 0.4154 r_free = 0.4154 target = 0.177115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.139615 restraints weight = 4527.319| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.05 r_work: 0.2938 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4444 Z= 0.168 Angle : 0.841 22.029 6060 Z= 0.381 Chirality : 0.052 0.567 671 Planarity : 0.005 0.065 733 Dihedral : 8.076 84.566 603 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.43 % Allowed : 18.81 % Favored : 78.76 % Cbeta Deviations : 0.21 % 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: 1.31 (0.38), residues: 530 helix: 1.45 (0.26), residues: 411 sheet: None (None), residues: 0 loop : -1.11 (0.59), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 69 TYR 0.026 0.001 TYR A 60 PHE 0.011 0.001 PHE A 385 TRP 0.020 0.001 TRP A 230 HIS 0.001 0.000 HIS A 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.17 ( 4440) covalent geometry : angle 0.71536 / 0.35 ( 6049) SS BOND : bond 0.00295 / 0.18 ( 1) SS BOND : angle 1.28876 / 0.45 ( 2) hydrogen bonds : bond 0.04802 / 3.11 ( 282) hydrogen bonds : angle 4.53920 / 3.25 ( 837) link_NAG-ASN : bond 0.00612 / 0.34 ( 3) link_NAG-ASN : angle 11.46370 / 5.37 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1263.60 seconds wall clock time: 22 minutes 17.95 seconds (1337.95 seconds total)