Starting phenix.real_space_refine on Thu Jul 2 02:27:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rxh_24731/07_2026/7rxh_24731_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rxh_24731/07_2026/7rxh_24731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rxh_24731/07_2026/7rxh_24731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rxh_24731/07_2026/7rxh_24731.map" model { file = "/net/cci-nas-00/data/ceres_data/7rxh_24731/07_2026/7rxh_24731_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rxh_24731/07_2026/7rxh_24731_neut.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 P 15 5.49 5 S 18 5.16 5 C 3653 2.51 5 N 849 2.21 5 O 1046 1.98 5 H 48 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s 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: 5631 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5062 Classifications: {'peptide': 626} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 30, 'TRANS': 595} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 65 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 52 Chain: "A" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 567 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'PGW': 16} Classifications: {'undetermined': 16, 'water': 24} Link IDs: {None: 39} Chain breaks: 2 Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 338 Unresolved non-hydrogen dihedrals: 357 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'PGW:plan-3': 10, 'PGW:plan-2': 1} Unresolved non-hydrogen planarities: 37 Time building chain proxies: 1.41, per 1000 atoms: 0.25 Number of scatterers: 5631 At special positions: 0 Unit cell: (72.7901, 85.5107, 98.938, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 2 19.99 S 18 16.00 P 15 15.00 O 1046 8.00 N 849 7.00 C 3653 6.00 H 48 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 179.5 milliseconds 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1200 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 3 sheets defined 73.3% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 28 through 46 Processing helix chain 'A' and resid 68 through 86 Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 103 through 117 Processing helix chain 'A' and resid 118 through 122 Processing helix chain 'A' and resid 144 through 156 Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'A' and resid 174 through 191 Processing helix chain 'A' and resid 191 through 205 Processing helix chain 'A' and resid 209 through 238 Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 272 through 281 Processing helix chain 'A' and resid 282 through 311 Processing helix chain 'A' and resid 317 through 350 removed outlier: 4.462A pdb=" N ILE A 323 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Proline residue: A 324 - end of helix Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 354 through 384 removed outlier: 3.980A pdb=" N VAL A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 392 through 398 removed outlier: 4.124A pdb=" N ASP A 397 " --> pdb=" O PRO A 394 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL A 398 " --> pdb=" O TYR A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 removed outlier: 4.336A pdb=" N VAL A 403 " --> pdb=" O PHE A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 414 Processing helix chain 'A' and resid 424 through 435 Processing helix chain 'A' and resid 435 through 463 removed outlier: 4.735A pdb=" N VAL A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Proline residue: A 449 - end of helix Processing helix chain 'A' and resid 490 through 501 Processing helix chain 'A' and resid 507 through 526 removed outlier: 4.054A pdb=" N ASP A 511 " --> pdb=" O ASP A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 529 No H-bonds generated for 'chain 'A' and resid 527 through 529' Processing helix chain 'A' and resid 531 through 554 removed outlier: 3.787A pdb=" N ARG A 545 " --> pdb=" O TRP A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 591 removed outlier: 4.419A pdb=" N ASP A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 582 " --> pdb=" O TRP A 578 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 634 removed outlier: 3.528A pdb=" N LYS A 634 " --> pdb=" O SER A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 658 Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 54 removed outlier: 3.764A pdb=" N ALA A 138 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASN A 23 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N VAL A 136 " --> pdb=" O ASN A 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 260 through 261 removed outlier: 4.119A pdb=" N GLU A 266 " --> pdb=" O ASP A 261 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 504 through 505 removed outlier: 6.672A pdb=" N GLU A 504 " --> pdb=" O LYS A 556 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 347 hydrogen bonds defined for protein. 1011 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: 0.87 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 48 1.03 - 1.22: 33 1.22 - 1.42: 2317 1.42 - 1.61: 3274 1.61 - 1.81: 52 Bond restraints: 5724 Sorted by residual: bond pdb=" C1 PGW A 810 " pdb=" O01 PGW A 810 " ideal model delta sigma weight residual 1.332 1.426 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C1 PGW A 807 " pdb=" O01 PGW A 807 " ideal model delta sigma weight residual 1.332 1.422 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C1 PGW A 809 " pdb=" O01 PGW A 809 " ideal model delta sigma weight residual 1.332 1.422 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C1 PGW A 817 " pdb=" O01 PGW A 817 " ideal model delta sigma weight residual 1.332 1.421 -0.089 2.00e-02 2.50e+03 1.96e+01 bond pdb=" C1 PGW A 814 " pdb=" O01 PGW A 814 " ideal model delta sigma weight residual 1.332 1.420 -0.088 2.00e-02 2.50e+03 1.93e+01 ... (remaining 5719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 7127 2.29 - 4.58: 342 4.58 - 6.87: 124 6.87 - 9.16: 20 9.16 - 11.45: 39 Bond angle restraints: 7652 Sorted by residual: angle pdb=" N ARG A 404 " pdb=" CA ARG A 404 " pdb=" C ARG A 404 " ideal model delta sigma weight residual 113.16 119.81 -6.65 1.42e+00 4.96e-01 2.19e+01 angle pdb=" N GLU A 418 " pdb=" CA GLU A 418 " pdb=" C GLU A 418 " ideal model delta sigma weight residual 109.96 103.92 6.04 1.50e+00 4.44e-01 1.62e+01 angle pdb=" C ARG A 404 " pdb=" N PRO A 405 " pdb=" CA PRO A 405 " ideal model delta sigma weight residual 119.84 114.93 4.91 1.25e+00 6.40e-01 1.54e+01 angle pdb=" O11 PGW A 807 " pdb=" P PGW A 807 " pdb=" O12 PGW A 807 " ideal model delta sigma weight residual 98.90 110.35 -11.45 3.00e+00 1.11e-01 1.46e+01 angle pdb=" N ILE A 421 " pdb=" CA ILE A 421 " pdb=" C ILE A 421 " ideal model delta sigma weight residual 109.51 114.97 -5.46 1.43e+00 4.89e-01 1.46e+01 ... (remaining 7647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.98: 3238 34.98 - 69.95: 182 69.95 - 104.93: 35 104.93 - 139.90: 8 139.90 - 174.87: 11 Dihedral angle restraints: 3474 sinusoidal: 1624 harmonic: 1850 Sorted by residual: dihedral pdb=" CA ALA A 389 " pdb=" C ALA A 389 " pdb=" N SER A 390 " pdb=" CA SER A 390 " ideal model delta harmonic sigma weight residual 180.00 153.91 26.09 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" O01 PGW A 810 " pdb=" C01 PGW A 810 " pdb=" C02 PGW A 810 " pdb=" O03 PGW A 810 " ideal model delta sinusoidal sigma weight residual 59.30 -115.57 174.87 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C03 PGW A 810 " pdb=" C01 PGW A 810 " pdb=" C02 PGW A 810 " pdb=" O03 PGW A 810 " ideal model delta sinusoidal sigma weight residual 295.35 121.86 173.49 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 3471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 707 0.068 - 0.136: 88 0.136 - 0.203: 16 0.203 - 0.271: 0 0.271 - 0.339: 1 Chirality restraints: 812 Sorted by residual: chirality pdb=" CA ARG A 404 " pdb=" N ARG A 404 " pdb=" C ARG A 404 " pdb=" CB ARG A 404 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CA ILE A 421 " pdb=" N ILE A 421 " pdb=" C ILE A 421 " pdb=" CB ILE A 421 " both_signs ideal model delta sigma weight residual False 2.43 2.25 0.19 2.00e-01 2.50e+01 8.65e-01 chirality pdb=" C02 PGW A 813 " pdb=" C01 PGW A 813 " pdb=" C03 PGW A 813 " pdb=" O01 PGW A 813 " both_signs ideal model delta sigma weight residual False 2.36 2.54 -0.18 2.00e-01 2.50e+01 8.11e-01 ... (remaining 809 not shown) Planarity restraints: 930 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 352 " -0.010 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" C TYR A 352 " 0.033 2.00e-02 2.50e+03 pdb=" O TYR A 352 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU A 353 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 393 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.26e+00 pdb=" N PRO A 394 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 394 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 394 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 526 " 0.029 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO A 527 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " 0.024 5.00e-02 4.00e+02 ... (remaining 927 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.30: 30 2.30 - 2.87: 2026 2.87 - 3.45: 6618 3.45 - 4.02: 11498 4.02 - 4.60: 16821 Nonbonded interactions: 36993 Sorted by model distance: nonbonded pdb=" OG SER A 546 " pdb=" H1 HOH A2702 " model vdw 1.723 2.450 nonbonded pdb=" O LYS A 556 " pdb=" H1 HOH A2709 " model vdw 1.739 2.450 nonbonded pdb=" OH TYR A 621 " pdb=" H1 HOH A2704 " model vdw 1.740 2.450 nonbonded pdb=" OG1 THR A 116 " pdb=" H1 HOH A2705 " model vdw 1.769 2.450 nonbonded pdb=" OD2 ASP A 233 " pdb=" H1 HOH A2703 " model vdw 1.778 2.450 ... (remaining 36988 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: 5.050 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: 0.050 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.860 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 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 : 0.009 0.094 5676 Z= 0.433 Angle : 1.403 11.447 7628 Z= 0.571 Chirality : 0.050 0.339 812 Planarity : 0.005 0.045 930 Dihedral : 24.726 174.875 2274 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.73 % Favored : 97.11 % Rotamer: Outliers : 0.56 % Allowed : 2.22 % Favored : 97.22 % 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: -0.87 (0.31), residues: 622 helix: 0.09 (0.22), residues: 424 sheet: -0.80 (0.80), residues: 27 loop : -2.04 (0.45), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 496 TYR 0.013 0.002 TYR A 352 PHE 0.018 0.002 PHE A 388 TRP 0.028 0.003 TRP A 155 HIS 0.008 0.002 HIS A 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00872 / 0.43 ( 5676) covalent geometry : angle 1.40329 / 0.57 ( 7628) hydrogen bonds : bond 0.10973 / 7.17 ( 347) hydrogen bonds : angle 5.47823 / 3.95 ( 1011) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 91 time to evaluate : 0.201 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 92 average time/residue: 0.5502 time to fit residues: 52.7947 Evaluate side-chains 51 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 GLN ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN A 171 ASN A 283 GLN A 370 ASN A 438 GLN A 453 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.103390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.073862 restraints weight = 8221.439| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.02 r_work: 0.2711 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5676 Z= 0.160 Angle : 0.582 6.358 7628 Z= 0.291 Chirality : 0.039 0.164 812 Planarity : 0.004 0.035 930 Dihedral : 24.904 169.417 1100 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.04 % Allowed : 10.56 % Favored : 87.41 % 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: 0.86 (0.33), residues: 622 helix: 1.44 (0.24), residues: 426 sheet: 0.01 (1.00), residues: 22 loop : -1.56 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 562 TYR 0.017 0.001 TYR A 180 PHE 0.011 0.001 PHE A 193 TRP 0.032 0.002 TRP A 155 HIS 0.003 0.001 HIS A 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 ( 5676) covalent geometry : angle 0.58160 / 0.29 ( 7628) hydrogen bonds : bond 0.04597 / 2.95 ( 347) hydrogen bonds : angle 4.32307 / 3.12 ( 1011) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.205 Fit side-chains REVERT: A 28 ASP cc_start: 0.7729 (t0) cc_final: 0.6969 (t0) REVERT: A 104 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7782 (tt0) outliers start: 11 outliers final: 4 residues processed: 56 average time/residue: 0.5389 time to fit residues: 31.7266 Evaluate side-chains 44 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 592 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 0 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 54 GLN A 113 HIS A 230 GLN A 539 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.097191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.067678 restraints weight = 8190.694| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 2.00 r_work: 0.2581 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2434 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9029 moved from start: 0.5150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5676 Z= 0.189 Angle : 0.508 5.603 7628 Z= 0.275 Chirality : 0.040 0.157 812 Planarity : 0.004 0.034 930 Dihedral : 21.952 173.691 1100 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.78 % Allowed : 10.37 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.34), residues: 622 helix: 2.02 (0.25), residues: 425 sheet: 0.50 (1.02), residues: 22 loop : -1.20 (0.47), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 642 TYR 0.017 0.002 TYR A 212 PHE 0.013 0.001 PHE A 193 TRP 0.035 0.002 TRP A 155 HIS 0.007 0.001 HIS A 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 ( 5676) covalent geometry : angle 0.50807 / 0.28 ( 7628) hydrogen bonds : bond 0.05183 / 3.34 ( 347) hydrogen bonds : angle 4.31806 / 3.10 ( 1011) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.255 Fit side-chains REVERT: A 28 ASP cc_start: 0.7989 (t0) cc_final: 0.7218 (t0) REVERT: A 104 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8238 (tt0) REVERT: A 146 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8656 (tp30) REVERT: A 592 SER cc_start: 0.8900 (OUTLIER) cc_final: 0.8669 (p) REVERT: A 647 ARG cc_start: 0.7494 (tpt170) cc_final: 0.7055 (ttp80) outliers start: 15 outliers final: 2 residues processed: 49 average time/residue: 0.6252 time to fit residues: 32.0810 Evaluate side-chains 38 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 658 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 38 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 37 optimal weight: 0.0040 chunk 23 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.098961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.069841 restraints weight = 8229.261| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 2.01 r_work: 0.2631 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2488 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5676 Z= 0.120 Angle : 0.426 4.611 7628 Z= 0.229 Chirality : 0.037 0.142 812 Planarity : 0.003 0.030 930 Dihedral : 19.702 179.181 1098 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.04 % Allowed : 9.63 % Favored : 88.33 % 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: 2.16 (0.35), residues: 622 helix: 2.42 (0.25), residues: 425 sheet: 0.78 (1.07), residues: 22 loop : -1.05 (0.48), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 642 TYR 0.011 0.001 TYR A 180 PHE 0.007 0.001 PHE A 193 TRP 0.028 0.002 TRP A 155 HIS 0.003 0.001 HIS A 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 5676) covalent geometry : angle 0.42640 / 0.23 ( 7628) hydrogen bonds : bond 0.04146 / 2.64 ( 347) hydrogen bonds : angle 3.98107 / 2.85 ( 1011) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.215 Fit side-chains REVERT: A 28 ASP cc_start: 0.7829 (t0) cc_final: 0.7309 (t0) REVERT: A 56 ASP cc_start: 0.7665 (m-30) cc_final: 0.7436 (m-30) REVERT: A 104 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8119 (tt0) REVERT: A 146 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8547 (tp30) REVERT: A 305 GLU cc_start: 0.8975 (tp30) cc_final: 0.8683 (tt0) REVERT: A 420 SER cc_start: 0.7893 (t) cc_final: 0.7494 (p) REVERT: A 647 ARG cc_start: 0.7459 (tpt170) cc_final: 0.7030 (ttp80) outliers start: 11 outliers final: 2 residues processed: 51 average time/residue: 0.5425 time to fit residues: 29.0920 Evaluate side-chains 43 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 353 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 39 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.094098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.064895 restraints weight = 8330.073| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 2.00 r_work: 0.2534 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2389 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9073 moved from start: 0.5877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5676 Z= 0.225 Angle : 0.510 5.326 7628 Z= 0.280 Chirality : 0.041 0.165 812 Planarity : 0.004 0.030 930 Dihedral : 19.031 178.870 1098 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.41 % Allowed : 9.81 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.35), residues: 622 helix: 2.24 (0.25), residues: 424 sheet: 0.42 (1.05), residues: 24 loop : -0.88 (0.49), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 268 TYR 0.018 0.002 TYR A 212 PHE 0.015 0.002 PHE A 419 TRP 0.031 0.002 TRP A 155 HIS 0.008 0.001 HIS A 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.22 ( 5676) covalent geometry : angle 0.50966 / 0.28 ( 7628) hydrogen bonds : bond 0.05422 / 3.49 ( 347) hydrogen bonds : angle 4.28599 / 3.10 ( 1011) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.211 Fit side-chains REVERT: A 28 ASP cc_start: 0.7998 (t0) cc_final: 0.7539 (t0) REVERT: A 104 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8220 (tt0) REVERT: A 146 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8584 (tp30) REVERT: A 211 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8856 (tp) REVERT: A 305 GLU cc_start: 0.8981 (tp30) cc_final: 0.8684 (tt0) REVERT: A 454 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7415 (tpt170) REVERT: A 647 ARG cc_start: 0.7491 (tpt170) cc_final: 0.7062 (ttp80) outliers start: 13 outliers final: 2 residues processed: 49 average time/residue: 0.6262 time to fit residues: 31.9790 Evaluate side-chains 42 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 659 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 1 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 31 optimal weight: 0.0010 chunk 55 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.095945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.066721 restraints weight = 8239.529| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 2.02 r_work: 0.2573 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2428 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9048 moved from start: 0.5974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5676 Z= 0.147 Angle : 0.439 5.199 7628 Z= 0.239 Chirality : 0.038 0.145 812 Planarity : 0.003 0.029 930 Dihedral : 17.869 176.284 1098 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.22 % Allowed : 10.74 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.35), residues: 622 helix: 2.46 (0.26), residues: 424 sheet: 0.50 (1.08), residues: 24 loop : -0.88 (0.50), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 268 TYR 0.011 0.001 TYR A 212 PHE 0.008 0.001 PHE A 193 TRP 0.025 0.002 TRP A 155 HIS 0.005 0.001 HIS A 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 5676) covalent geometry : angle 0.43854 / 0.24 ( 7628) hydrogen bonds : bond 0.04521 / 2.88 ( 347) hydrogen bonds : angle 4.07127 / 2.92 ( 1011) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.221 Fit side-chains REVERT: A 28 ASP cc_start: 0.8042 (t0) cc_final: 0.7545 (t0) REVERT: A 104 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8157 (tt0) REVERT: A 211 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8770 (tp) REVERT: A 305 GLU cc_start: 0.8948 (tp30) cc_final: 0.8746 (tt0) REVERT: A 420 SER cc_start: 0.8100 (t) cc_final: 0.7657 (p) REVERT: A 454 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7433 (tpt170) REVERT: A 647 ARG cc_start: 0.7502 (tpt170) cc_final: 0.7075 (ttp80) outliers start: 12 outliers final: 2 residues processed: 51 average time/residue: 0.5159 time to fit residues: 27.5562 Evaluate side-chains 45 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 454 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.092474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.063528 restraints weight = 8366.844| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 1.99 r_work: 0.2509 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2364 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9092 moved from start: 0.6073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 5676 Z= 0.332 Angle : 0.559 5.299 7628 Z= 0.304 Chirality : 0.044 0.181 812 Planarity : 0.004 0.028 930 Dihedral : 18.516 178.225 1098 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.04 % Allowed : 10.56 % Favored : 87.41 % 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: 1.95 (0.35), residues: 622 helix: 2.22 (0.25), residues: 424 sheet: 0.58 (1.05), residues: 24 loop : -1.00 (0.49), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 642 TYR 0.017 0.002 TYR A 212 PHE 0.017 0.002 PHE A 193 TRP 0.031 0.002 TRP A 155 HIS 0.008 0.001 HIS A 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00768 / 0.33 ( 5676) covalent geometry : angle 0.55939 / 0.30 ( 7628) hydrogen bonds : bond 0.05691 / 3.67 ( 347) hydrogen bonds : angle 4.34902 / 3.14 ( 1011) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.151 Fit side-chains REVERT: A 28 ASP cc_start: 0.8140 (t0) cc_final: 0.7702 (t0) REVERT: A 104 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8257 (tt0) REVERT: A 211 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8881 (tp) REVERT: A 305 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8694 (tt0) REVERT: A 454 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7579 (mmt-90) REVERT: A 647 ARG cc_start: 0.7514 (tpt170) cc_final: 0.7073 (ttp80) outliers start: 11 outliers final: 4 residues processed: 47 average time/residue: 0.5560 time to fit residues: 27.1787 Evaluate side-chains 45 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 659 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.095214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.066328 restraints weight = 8228.538| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 2.01 r_work: 0.2568 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2423 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9040 moved from start: 0.6150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5676 Z= 0.152 Angle : 0.450 5.947 7628 Z= 0.245 Chirality : 0.038 0.147 812 Planarity : 0.003 0.027 930 Dihedral : 17.539 174.449 1098 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.85 % Allowed : 10.37 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.35), residues: 622 helix: 2.44 (0.25), residues: 423 sheet: 0.50 (1.07), residues: 24 loop : -0.90 (0.50), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 642 TYR 0.011 0.001 TYR A 212 PHE 0.008 0.001 PHE A 193 TRP 0.024 0.002 TRP A 155 HIS 0.005 0.001 HIS A 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 5676) covalent geometry : angle 0.45015 / 0.25 ( 7628) hydrogen bonds : bond 0.04627 / 2.95 ( 347) hydrogen bonds : angle 4.12218 / 2.96 ( 1011) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.202 Fit side-chains REVERT: A 28 ASP cc_start: 0.8135 (t0) cc_final: 0.7720 (t0) REVERT: A 104 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8157 (tt0) REVERT: A 211 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8759 (tp) REVERT: A 420 SER cc_start: 0.8279 (t) cc_final: 0.7843 (p) REVERT: A 454 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7498 (tpt170) REVERT: A 647 ARG cc_start: 0.7495 (tpt170) cc_final: 0.7046 (ttp80) outliers start: 10 outliers final: 4 residues processed: 47 average time/residue: 0.6016 time to fit residues: 29.4676 Evaluate side-chains 44 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 659 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.093998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.065122 restraints weight = 8277.672| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 2.00 r_work: 0.2541 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2396 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9073 moved from start: 0.6213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5676 Z= 0.203 Angle : 0.484 5.787 7628 Z= 0.265 Chirality : 0.040 0.158 812 Planarity : 0.003 0.028 930 Dihedral : 17.076 172.576 1098 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.67 % Allowed : 10.93 % Favored : 87.41 % 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: 2.16 (0.35), residues: 622 helix: 2.41 (0.25), residues: 423 sheet: 0.59 (1.06), residues: 24 loop : -0.99 (0.50), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 642 TYR 0.015 0.001 TYR A 212 PHE 0.012 0.001 PHE A 193 TRP 0.026 0.002 TRP A 155 HIS 0.006 0.001 HIS A 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 ( 5676) covalent geometry : angle 0.48389 / 0.26 ( 7628) hydrogen bonds : bond 0.05032 / 3.23 ( 347) hydrogen bonds : angle 4.19053 / 3.01 ( 1011) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.161 Fit side-chains REVERT: A 28 ASP cc_start: 0.8140 (t0) cc_final: 0.7748 (t0) REVERT: A 104 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8213 (tt0) REVERT: A 211 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8814 (tp) REVERT: A 454 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7546 (tpt170) REVERT: A 647 ARG cc_start: 0.7497 (tpt170) cc_final: 0.7075 (ttp80) outliers start: 9 outliers final: 5 residues processed: 44 average time/residue: 0.5903 time to fit residues: 27.0044 Evaluate side-chains 47 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 659 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 14 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.095086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.065893 restraints weight = 8305.738| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 2.03 r_work: 0.2561 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2414 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9048 moved from start: 0.6267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5676 Z= 0.164 Angle : 0.447 6.278 7628 Z= 0.244 Chirality : 0.038 0.149 812 Planarity : 0.003 0.027 930 Dihedral : 16.253 167.647 1098 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.48 % Allowed : 11.30 % Favored : 87.22 % 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: 2.34 (0.35), residues: 622 helix: 2.54 (0.25), residues: 423 sheet: 0.65 (1.07), residues: 24 loop : -0.87 (0.50), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 642 TYR 0.011 0.001 TYR A 180 PHE 0.009 0.001 PHE A 181 TRP 0.024 0.002 TRP A 155 HIS 0.005 0.001 HIS A 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 5676) covalent geometry : angle 0.44700 / 0.24 ( 7628) hydrogen bonds : bond 0.04572 / 2.91 ( 347) hydrogen bonds : angle 4.08878 / 2.93 ( 1011) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.135 Fit side-chains REVERT: A 28 ASP cc_start: 0.8104 (t0) cc_final: 0.7719 (t0) REVERT: A 104 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8189 (tt0) REVERT: A 211 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8735 (tp) REVERT: A 420 SER cc_start: 0.8219 (t) cc_final: 0.7796 (p) REVERT: A 454 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7528 (tpt170) REVERT: A 647 ARG cc_start: 0.7517 (tpt170) cc_final: 0.7078 (ttp80) outliers start: 8 outliers final: 4 residues processed: 48 average time/residue: 0.6630 time to fit residues: 33.0172 Evaluate side-chains 49 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 659 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 30 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 56 optimal weight: 0.0980 chunk 42 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.097059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.068398 restraints weight = 8159.773| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 2.00 r_work: 0.2607 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2464 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 moved from start: 0.6335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5676 Z= 0.114 Angle : 0.421 6.254 7628 Z= 0.228 Chirality : 0.037 0.135 812 Planarity : 0.003 0.027 930 Dihedral : 15.163 159.544 1098 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.30 % Allowed : 11.67 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.36), residues: 622 helix: 2.70 (0.26), residues: 427 sheet: 0.79 (1.10), residues: 24 loop : -0.90 (0.51), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 492 TYR 0.011 0.001 TYR A 180 PHE 0.006 0.001 PHE A 193 TRP 0.022 0.002 TRP A 155 HIS 0.004 0.001 HIS A 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 5676) covalent geometry : angle 0.42066 / 0.23 ( 7628) hydrogen bonds : bond 0.04101 / 2.61 ( 347) hydrogen bonds : angle 3.94844 / 2.82 ( 1011) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2115.90 seconds wall clock time: 36 minutes 46.25 seconds (2206.25 seconds total)