Starting phenix.real_space_refine on Tue Mar 3 12:38:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y7v_33671/03_2026/7y7v_33671.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y7v_33671/03_2026/7y7v_33671.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y7v_33671/03_2026/7y7v_33671.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y7v_33671/03_2026/7y7v_33671.map" model { file = "/net/cci-nas-00/data/ceres_data/7y7v_33671/03_2026/7y7v_33671.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y7v_33671/03_2026/7y7v_33671.cif" } resolution = 2.2 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= -0.001 sd= 0.111 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 34 5.16 5 Cl 1 4.86 5 C 2861 2.51 5 N 659 2.21 5 O 786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4341 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4240 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 22, 'TRANS': 509} Chain: "A" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 101 Unusual residues: {' CL': 1, 'NAG': 3} Classifications: {'undetermined': 4, 'water': 58} Link IDs: {None: 61} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.37, per 1000 atoms: 0.32 Number of scatterers: 4341 At special positions: 0 Unit cell: (69.28, 71.445, 97.425, 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 34 16.00 O 786 8.00 N 659 7.00 C 2861 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=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 181 " " NAG A 702 " - " ASN A 176 " " NAG A 703 " - " ASN A 184 " Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 363.4 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: 32 helices and 1 sheets defined 82.1% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 46 through 57 Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.531A pdb=" N VAL A 67 " --> pdb=" O GLY A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 77 removed outlier: 3.702A pdb=" N TYR A 72 " --> pdb=" O TRP A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 81 removed outlier: 4.763A pdb=" N ALA A 81 " --> pdb=" O GLY A 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 78 through 81' Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 93 through 109 Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.798A pdb=" N TRP A 116 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS A 117 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 122 through 154 removed outlier: 4.031A pdb=" N GLY A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE A 143 " --> pdb=" O TYR A 139 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 211 through 230 Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.599A pdb=" N THR A 236 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 259 Proline residue: A 247 - end of helix Processing helix chain 'A' and resid 263 through 273 Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.709A pdb=" N SER A 280 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 297 removed outlier: 3.996A pdb=" N TRP A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 310 removed outlier: 3.615A pdb=" N TYR A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 350 removed outlier: 3.664A pdb=" N ASP A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 363 through 374 Proline residue: A 369 - end of helix Processing helix chain 'A' and resid 377 through 412 removed outlier: 3.727A 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 436 Processing helix chain 'A' and resid 437 through 439 No H-bonds generated for 'chain 'A' and resid 437 through 439' Processing helix chain 'A' and resid 442 through 454 removed outlier: 3.900A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 473 removed outlier: 3.775A pdb=" N ILE A 471 " --> pdb=" O GLU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 489 Processing helix chain 'A' and resid 493 through 502 removed outlier: 4.262A pdb=" N LYS A 497 " --> pdb=" O CYS A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 519 Processing helix chain 'A' and resid 530 through 546 removed outlier: 4.004A pdb=" N SER A 544 " --> pdb=" O MET A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 559 Processing helix chain 'A' and resid 562 through 572 Processing sheet with id=AA1, first strand: chain 'A' and resid 523 through 524 290 hydrogen bonds defined for protein. 852 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: 0.64 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 717 1.33 - 1.46: 1744 1.46 - 1.59: 1904 1.59 - 1.73: 0 1.73 - 1.86: 54 Bond restraints: 4419 Sorted by residual: bond pdb=" C ARG A 172 " pdb=" O ARG A 172 " ideal model delta sigma weight residual 1.235 1.194 0.042 1.33e-02 5.65e+03 9.84e+00 bond pdb=" C ASP A 171 " pdb=" N ARG A 172 " ideal model delta sigma weight residual 1.331 1.305 0.026 1.43e-02 4.89e+03 3.40e+00 bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.16e+00 bond pdb=" C1 NAG A 703 " pdb=" O5 NAG A 703 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.01e+00 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.90e+00 ... (remaining 4414 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 5911 2.26 - 4.52: 96 4.52 - 6.78: 11 6.78 - 9.04: 1 9.04 - 11.30: 1 Bond angle restraints: 6020 Sorted by residual: angle pdb=" OG1 THR A 406 " pdb=" CB THR A 406 " pdb=" CG2 THR A 406 " ideal model delta sigma weight residual 109.30 120.60 -11.30 2.00e+00 2.50e-01 3.19e+01 angle pdb=" CA THR A 406 " pdb=" CB THR A 406 " pdb=" CG2 THR A 406 " ideal model delta sigma weight residual 110.50 118.65 -8.15 1.70e+00 3.46e-01 2.30e+01 angle pdb=" CA THR A 406 " pdb=" CB THR A 406 " pdb=" OG1 THR A 406 " ideal model delta sigma weight residual 109.60 115.67 -6.07 1.50e+00 4.44e-01 1.64e+01 angle pdb=" CA ARG A 172 " pdb=" C ARG A 172 " pdb=" O ARG A 172 " ideal model delta sigma weight residual 119.43 114.55 4.88 1.21e+00 6.83e-01 1.63e+01 angle pdb=" N ASP A 52 " pdb=" CA ASP A 52 " pdb=" C ASP A 52 " ideal model delta sigma weight residual 111.28 115.47 -4.19 1.09e+00 8.42e-01 1.48e+01 ... (remaining 6015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.28: 2160 16.28 - 32.57: 264 32.57 - 48.85: 83 48.85 - 65.14: 19 65.14 - 81.42: 5 Dihedral angle restraints: 2531 sinusoidal: 999 harmonic: 1532 Sorted by residual: dihedral pdb=" CA GLY A 111 " pdb=" C GLY A 111 " pdb=" N GLY A 112 " pdb=" CA GLY A 112 " ideal model delta harmonic sigma weight residual 180.00 -159.61 -20.39 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA GLN A 199 " pdb=" C GLN A 199 " pdb=" N MET A 200 " pdb=" CA MET A 200 " ideal model delta harmonic sigma weight residual 180.00 -159.74 -20.26 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA TYR A 453 " pdb=" C TYR A 453 " pdb=" N SER A 454 " pdb=" CA SER A 454 " ideal model delta harmonic sigma weight residual 180.00 -159.98 -20.02 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 2528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.283: 667 0.283 - 0.565: 2 0.565 - 0.848: 0 0.848 - 1.131: 0 1.131 - 1.413: 1 Chirality restraints: 670 Sorted by residual: chirality pdb=" CB THR A 406 " pdb=" CA THR A 406 " pdb=" OG1 THR A 406 " pdb=" CG2 THR A 406 " both_signs ideal model delta sigma weight residual False 2.55 1.14 1.41 2.00e-01 2.50e+01 4.99e+01 chirality pdb=" CA ASP A 52 " pdb=" N ASP A 52 " pdb=" C ASP A 52 " pdb=" CB ASP A 52 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 176 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.75 0.35 2.00e-01 2.50e+01 3.00e+00 ... (remaining 667 not shown) Planarity restraints: 731 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 184 " 0.157 2.00e-02 2.50e+03 1.65e-01 3.38e+02 pdb=" CG ASN A 184 " -0.059 2.00e-02 2.50e+03 pdb=" OD1 ASN A 184 " -0.059 2.00e-02 2.50e+03 pdb=" ND2 ASN A 184 " -0.246 2.00e-02 2.50e+03 pdb=" C1 NAG A 703 " 0.207 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 181 " -0.031 2.00e-02 2.50e+03 3.38e-02 1.42e+01 pdb=" CG ASN A 181 " 0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN A 181 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 181 " 0.055 2.00e-02 2.50e+03 pdb=" C1 NAG A 701 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 176 " 0.024 2.00e-02 2.50e+03 2.51e-02 7.87e+00 pdb=" CG ASN A 176 " -0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN A 176 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A 176 " -0.038 2.00e-02 2.50e+03 pdb=" C1 NAG A 702 " 0.031 2.00e-02 2.50e+03 ... (remaining 728 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 50 2.64 - 3.21: 4207 3.21 - 3.77: 7211 3.77 - 4.34: 10093 4.34 - 4.90: 15768 Nonbonded interactions: 37329 Sorted by model distance: nonbonded pdb=" O SER A 243 " pdb=" O HOH A 801 " model vdw 2.078 3.040 nonbonded pdb=" OH TYR A 140 " pdb=" O HOH A 802 " model vdw 2.079 3.040 nonbonded pdb=" O MET A 570 " pdb=" O HOH A 803 " model vdw 2.151 3.040 nonbonded pdb=" OD1 ASN A 184 " pdb=" O5 NAG A 703 " model vdw 2.209 3.040 nonbonded pdb=" O LYS A 564 " pdb=" OE1 GLN A 568 " model vdw 2.252 3.040 ... (remaining 37324 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.610 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:8.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 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 0.121 4423 Z= 0.259 Angle : 0.782 12.420 6031 Z= 0.417 Chirality : 0.073 1.413 670 Planarity : 0.005 0.033 728 Dihedral : 16.081 81.423 1556 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.11 % Allowed : 22.35 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.34), residues: 530 helix: 0.62 (0.25), residues: 382 sheet: None (None), residues: 0 loop : -1.26 (0.47), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.002 ARG A 50 TYR 0.024 0.002 TYR A 72 PHE 0.022 0.003 PHE A 339 TRP 0.013 0.002 TRP A 116 HIS 0.002 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 4419) covalent geometry : angle 0.72606 ( 6020) SS BOND : bond 0.00695 ( 1) SS BOND : angle 5.97461 ( 2) hydrogen bonds : bond 0.13768 ( 290) hydrogen bonds : angle 6.58099 ( 852) link_NAG-ASN : bond 0.09672 ( 3) link_NAG-ASN : angle 7.05430 ( 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 70 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.127 Fit side-chains REVERT: A 568 GLN cc_start: 0.7303 (mp10) cc_final: 0.6874 (tp40) outliers start: 5 outliers final: 1 residues processed: 69 average time/residue: 0.5506 time to fit residues: 39.3797 Evaluate side-chains 65 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 418 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.128828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.095931 restraints weight = 4178.358| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.47 r_work: 0.3043 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4423 Z= 0.174 Angle : 0.667 10.892 6031 Z= 0.341 Chirality : 0.050 0.465 670 Planarity : 0.004 0.033 728 Dihedral : 6.485 58.602 641 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.87 % Allowed : 17.48 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.36), residues: 530 helix: 1.36 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -1.11 (0.48), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 479 TYR 0.021 0.002 TYR A 72 PHE 0.020 0.002 PHE A 339 TRP 0.015 0.002 TRP A 116 HIS 0.002 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 4419) covalent geometry : angle 0.62658 ( 6020) SS BOND : bond 0.00729 ( 1) SS BOND : angle 3.59675 ( 2) hydrogen bonds : bond 0.06332 ( 290) hydrogen bonds : angle 5.11068 ( 852) link_NAG-ASN : bond 0.01426 ( 3) link_NAG-ASN : angle 5.72721 ( 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 86 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: A 184 ASN cc_start: 0.5707 (OUTLIER) cc_final: 0.5249 (m110) REVERT: A 380 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8280 (tp) outliers start: 22 outliers final: 12 residues processed: 80 average time/residue: 0.5721 time to fit residues: 47.3380 Evaluate side-chains 70 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 564 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 12 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 0.0010 chunk 18 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 44 optimal weight: 0.0670 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 534 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.133335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.101085 restraints weight = 4205.884| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.47 r_work: 0.3123 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4423 Z= 0.123 Angle : 0.568 8.266 6031 Z= 0.287 Chirality : 0.044 0.341 670 Planarity : 0.004 0.029 728 Dihedral : 5.811 53.756 641 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.20 % Allowed : 17.26 % 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: 1.50 (0.37), residues: 530 helix: 1.70 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -1.05 (0.50), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 172 TYR 0.014 0.001 TYR A 72 PHE 0.016 0.001 PHE A 462 TRP 0.009 0.001 TRP A 532 HIS 0.001 0.000 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 4419) covalent geometry : angle 0.53891 ( 6020) SS BOND : bond 0.00639 ( 1) SS BOND : angle 3.25299 ( 2) hydrogen bonds : bond 0.04696 ( 290) hydrogen bonds : angle 4.64702 ( 852) link_NAG-ASN : bond 0.01383 ( 3) link_NAG-ASN : angle 4.41874 ( 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 77 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.159 Fit side-chains REVERT: A 231 LYS cc_start: 0.4600 (OUTLIER) cc_final: 0.4355 (pptt) REVERT: A 278 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8505 (tmtm) REVERT: A 380 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8224 (tp) REVERT: A 564 LYS cc_start: 0.7797 (tttp) cc_final: 0.7577 (tptp) outliers start: 19 outliers final: 8 residues processed: 74 average time/residue: 0.5669 time to fit residues: 43.4273 Evaluate side-chains 65 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 464 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 38 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.130659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.097859 restraints weight = 4162.634| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.47 r_work: 0.3073 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4423 Z= 0.141 Angle : 0.584 7.587 6031 Z= 0.304 Chirality : 0.045 0.330 670 Planarity : 0.004 0.035 728 Dihedral : 5.753 49.186 641 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.32 % Allowed : 17.70 % 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: 1.53 (0.36), residues: 530 helix: 1.72 (0.26), residues: 390 sheet: None (None), residues: 0 loop : -0.97 (0.49), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 69 TYR 0.020 0.002 TYR A 72 PHE 0.018 0.002 PHE A 339 TRP 0.012 0.001 TRP A 116 HIS 0.002 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 4419) covalent geometry : angle 0.57100 ( 6020) SS BOND : bond 0.00434 ( 1) SS BOND : angle 0.44225 ( 2) hydrogen bonds : bond 0.05436 ( 290) hydrogen bonds : angle 4.75908 ( 852) link_NAG-ASN : bond 0.00861 ( 3) link_NAG-ASN : angle 3.26582 ( 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 72 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: A 231 LYS cc_start: 0.4746 (OUTLIER) cc_final: 0.4485 (pptt) REVERT: A 278 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8551 (tmtm) REVERT: A 380 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8249 (tp) outliers start: 15 outliers final: 10 residues processed: 71 average time/residue: 0.5463 time to fit residues: 40.2191 Evaluate side-chains 68 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 464 VAL 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 41 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.130658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.098117 restraints weight = 4205.722| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.47 r_work: 0.3079 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4423 Z= 0.135 Angle : 0.584 9.467 6031 Z= 0.295 Chirality : 0.045 0.268 670 Planarity : 0.004 0.035 728 Dihedral : 5.587 46.063 641 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.20 % Allowed : 17.48 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.36), residues: 530 helix: 1.76 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -0.96 (0.50), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 417 TYR 0.018 0.002 TYR A 72 PHE 0.018 0.002 PHE A 339 TRP 0.011 0.001 TRP A 116 HIS 0.002 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 4419) covalent geometry : angle 0.57004 ( 6020) SS BOND : bond 0.00408 ( 1) SS BOND : angle 0.79282 ( 2) hydrogen bonds : bond 0.05246 ( 290) hydrogen bonds : angle 4.68943 ( 852) link_NAG-ASN : bond 0.01278 ( 3) link_NAG-ASN : angle 3.28384 ( 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 75 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 231 LYS cc_start: 0.4837 (OUTLIER) cc_final: 0.4569 (pptt) REVERT: A 278 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8541 (tmtm) REVERT: A 380 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8232 (tp) outliers start: 19 outliers final: 11 residues processed: 72 average time/residue: 0.5629 time to fit residues: 42.0750 Evaluate side-chains 76 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 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 13 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN A 568 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.127607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.094632 restraints weight = 4213.917| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.47 r_work: 0.3023 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4423 Z= 0.197 Angle : 0.664 9.343 6031 Z= 0.345 Chirality : 0.051 0.454 670 Planarity : 0.004 0.035 728 Dihedral : 5.377 46.075 641 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.98 % Allowed : 17.48 % 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: 1.33 (0.36), residues: 530 helix: 1.56 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -0.97 (0.49), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 211 TYR 0.024 0.002 TYR A 72 PHE 0.018 0.002 PHE A 386 TRP 0.016 0.002 TRP A 116 HIS 0.004 0.002 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 4419) covalent geometry : angle 0.64262 ( 6020) SS BOND : bond 0.00635 ( 1) SS BOND : angle 1.17274 ( 2) hydrogen bonds : bond 0.06628 ( 290) hydrogen bonds : angle 5.00161 ( 852) link_NAG-ASN : bond 0.01465 ( 3) link_NAG-ASN : angle 4.33001 ( 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 74 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.172 Fit side-chains REVERT: A 230 TRP cc_start: 0.5571 (OUTLIER) cc_final: 0.4531 (p-90) REVERT: A 231 LYS cc_start: 0.4830 (OUTLIER) cc_final: 0.4574 (pptt) REVERT: A 278 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8537 (tmtm) REVERT: A 380 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8321 (tp) REVERT: A 568 GLN cc_start: 0.7808 (mm110) cc_final: 0.7473 (mm-40) outliers start: 18 outliers final: 12 residues processed: 72 average time/residue: 0.6112 time to fit residues: 45.5851 Evaluate side-chains 70 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 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 31 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 51 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.130333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.097601 restraints weight = 4226.919| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.48 r_work: 0.3072 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4423 Z= 0.135 Angle : 0.584 10.205 6031 Z= 0.298 Chirality : 0.046 0.379 670 Planarity : 0.004 0.034 728 Dihedral : 5.113 49.128 641 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.54 % Allowed : 17.26 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.36), residues: 530 helix: 1.76 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -0.98 (0.50), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 351 TYR 0.018 0.002 TYR A 246 PHE 0.018 0.002 PHE A 339 TRP 0.011 0.001 TRP A 116 HIS 0.002 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 4419) covalent geometry : angle 0.55826 ( 6020) SS BOND : bond 0.00397 ( 1) SS BOND : angle 0.83505 ( 2) hydrogen bonds : bond 0.05279 ( 290) hydrogen bonds : angle 4.72588 ( 852) link_NAG-ASN : bond 0.01493 ( 3) link_NAG-ASN : angle 4.47653 ( 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 71 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.202 Fit side-chains REVERT: A 230 TRP cc_start: 0.5539 (OUTLIER) cc_final: 0.5214 (t60) REVERT: A 231 LYS cc_start: 0.5014 (OUTLIER) cc_final: 0.4705 (pptt) REVERT: A 278 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8533 (tmtm) REVERT: A 380 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8244 (tp) REVERT: A 574 SER cc_start: 0.7333 (t) cc_final: 0.7081 (p) outliers start: 16 outliers final: 10 residues processed: 69 average time/residue: 0.5254 time to fit residues: 37.6723 Evaluate side-chains 69 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 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 9 optimal weight: 4.9990 chunk 26 optimal weight: 0.1980 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 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 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.131587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.098959 restraints weight = 4237.792| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.48 r_work: 0.3090 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4423 Z= 0.127 Angle : 0.569 10.834 6031 Z= 0.288 Chirality : 0.045 0.374 670 Planarity : 0.004 0.034 728 Dihedral : 4.996 52.047 641 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.32 % Allowed : 17.70 % 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: 1.71 (0.37), residues: 530 helix: 1.84 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -0.91 (0.50), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 420 TYR 0.018 0.001 TYR A 246 PHE 0.017 0.002 PHE A 339 TRP 0.011 0.001 TRP A 116 HIS 0.001 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 4419) covalent geometry : angle 0.54082 ( 6020) SS BOND : bond 0.00332 ( 1) SS BOND : angle 0.82157 ( 2) hydrogen bonds : bond 0.04993 ( 290) hydrogen bonds : angle 4.64259 ( 852) link_NAG-ASN : bond 0.01233 ( 3) link_NAG-ASN : angle 4.61127 ( 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 72 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 231 LYS cc_start: 0.5248 (OUTLIER) cc_final: 0.4907 (pptt) REVERT: A 278 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8529 (tmtm) REVERT: A 380 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8226 (tp) REVERT: A 568 GLN cc_start: 0.7455 (mm-40) cc_final: 0.7039 (mp10) outliers start: 15 outliers final: 10 residues processed: 70 average time/residue: 0.5397 time to fit residues: 39.1921 Evaluate side-chains 68 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 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 48 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 418 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.128857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.095931 restraints weight = 4226.803| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.47 r_work: 0.3043 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4423 Z= 0.166 Angle : 0.621 11.045 6031 Z= 0.319 Chirality : 0.048 0.388 670 Planarity : 0.004 0.035 728 Dihedral : 4.632 26.111 639 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.32 % Allowed : 17.48 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.36), residues: 530 helix: 1.69 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -0.91 (0.49), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 211 TYR 0.024 0.002 TYR A 246 PHE 0.016 0.002 PHE A 339 TRP 0.014 0.002 TRP A 116 HIS 0.002 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 4419) covalent geometry : angle 0.59520 ( 6020) SS BOND : bond 0.00488 ( 1) SS BOND : angle 1.01331 ( 2) hydrogen bonds : bond 0.06008 ( 290) hydrogen bonds : angle 4.87883 ( 852) link_NAG-ASN : bond 0.01190 ( 3) link_NAG-ASN : angle 4.64416 ( 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 77 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.142 Fit side-chains REVERT: A 231 LYS cc_start: 0.5340 (OUTLIER) cc_final: 0.5063 (pptt) REVERT: A 278 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8536 (tmtm) REVERT: A 380 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8291 (tp) outliers start: 15 outliers final: 11 residues processed: 75 average time/residue: 0.6368 time to fit residues: 49.3277 Evaluate side-chains 69 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 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 9 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 0.1980 chunk 47 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.130746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.098012 restraints weight = 4238.473| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.48 r_work: 0.3075 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4423 Z= 0.133 Angle : 0.581 11.071 6031 Z= 0.296 Chirality : 0.045 0.381 670 Planarity : 0.004 0.034 728 Dihedral : 4.503 26.063 639 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.10 % Allowed : 17.70 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.37), residues: 530 helix: 1.81 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -0.87 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 211 TYR 0.022 0.002 TYR A 246 PHE 0.018 0.002 PHE A 339 TRP 0.011 0.001 TRP A 116 HIS 0.002 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 4419) covalent geometry : angle 0.55308 ( 6020) SS BOND : bond 0.00378 ( 1) SS BOND : angle 0.93998 ( 2) hydrogen bonds : bond 0.05209 ( 290) hydrogen bonds : angle 4.71938 ( 852) link_NAG-ASN : bond 0.01147 ( 3) link_NAG-ASN : angle 4.62476 ( 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 69 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: A 278 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8519 (tmtm) REVERT: A 380 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8250 (tp) REVERT: A 568 GLN cc_start: 0.7631 (mm-40) cc_final: 0.7151 (mp10) outliers start: 14 outliers final: 10 residues processed: 68 average time/residue: 0.5577 time to fit residues: 39.3358 Evaluate side-chains 67 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 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 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 4 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.128974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.096065 restraints weight = 4223.204| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.48 r_work: 0.3046 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4423 Z= 0.163 Angle : 0.621 11.030 6031 Z= 0.319 Chirality : 0.047 0.387 670 Planarity : 0.004 0.036 728 Dihedral : 4.618 25.901 639 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.10 % Allowed : 17.26 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.36), residues: 530 helix: 1.69 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -0.93 (0.49), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 211 TYR 0.026 0.002 TYR A 246 PHE 0.017 0.002 PHE A 339 TRP 0.013 0.002 TRP A 116 HIS 0.002 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 4419) covalent geometry : angle 0.59522 ( 6020) SS BOND : bond 0.00466 ( 1) SS BOND : angle 1.03603 ( 2) hydrogen bonds : bond 0.05966 ( 290) hydrogen bonds : angle 4.88237 ( 852) link_NAG-ASN : bond 0.01119 ( 3) link_NAG-ASN : angle 4.59766 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1979.80 seconds wall clock time: 34 minutes 23.91 seconds (2063.91 seconds total)