Starting phenix.real_space_refine on Fri Aug 22 14:03:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j77_36030/08_2025/8j77_36030.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j77_36030/08_2025/8j77_36030.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j77_36030/08_2025/8j77_36030.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j77_36030/08_2025/8j77_36030.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j77_36030/08_2025/8j77_36030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j77_36030/08_2025/8j77_36030.map" } resolution = 3.7 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= 0.157 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 19 5.16 5 C 2513 2.51 5 N 577 2.21 5 O 669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3778 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3732 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 22, 'TRANS': 470} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'CHT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.99, per 1000 atoms: 0.26 Number of scatterers: 3778 At special positions: 0 Unit cell: (86.1, 69.7, 91.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 19 16.00 O 669 8.00 N 577 7.00 C 2513 6.00 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG B 1 " - " ASN A 301 " Time building additional restraints: 0.26 Conformation dependent library (CDL) restraints added in 147.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 898 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 1 sheets defined 74.4% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 3 through 28 Processing helix chain 'A' and resid 49 through 63 removed outlier: 3.775A pdb=" N TRP A 62 " --> pdb=" O MET A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 77 Processing helix chain 'A' and resid 81 through 84 Processing helix chain 'A' and resid 85 through 103 removed outlier: 4.763A pdb=" N ILE A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 93 " --> pdb=" O ILE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 107 removed outlier: 3.514A pdb=" N ARG A 107 " --> pdb=" O LYS A 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 104 through 107' Processing helix chain 'A' and resid 114 through 122 removed outlier: 4.538A pdb=" N PHE A 118 " --> pdb=" O MET A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 158 removed outlier: 3.926A pdb=" N LEU A 129 " --> pdb=" O ARG A 125 " (cutoff:3.500A) Proline residue: A 133 - end of helix Processing helix chain 'A' and resid 161 through 179 Processing helix chain 'A' and resid 187 through 201 Processing helix chain 'A' and resid 216 through 220 removed outlier: 3.577A pdb=" N ALA A 219 " --> pdb=" O GLY A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 236 through 251 removed outlier: 3.945A pdb=" N LEU A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 263 removed outlier: 3.526A pdb=" N PHE A 258 " --> pdb=" O TRP A 254 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 262 " --> pdb=" O PHE A 258 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER A 263 " --> pdb=" O GLN A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 298 removed outlier: 3.912A pdb=" N ALA A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLN A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Proline residue: A 287 - end of helix removed outlier: 3.637A pdb=" N ILE A 291 " --> pdb=" O PRO A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 318 through 327 Processing helix chain 'A' and resid 329 through 367 removed outlier: 3.699A pdb=" N PHE A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE A 335 " --> pdb=" O TYR A 331 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY A 336 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP A 349 " --> pdb=" O MET A 345 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 397 Processing helix chain 'A' and resid 402 through 417 removed outlier: 4.261A pdb=" N TRP A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 426 Processing helix chain 'A' and resid 431 through 448 removed outlier: 3.746A pdb=" N ALA A 435 " --> pdb=" O ASN A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 502 Processing sheet with id=AA1, first strand: chain 'A' and resid 466 through 467 removed outlier: 3.752A pdb=" N ASN A 474 " --> pdb=" O TYR A 466 " (cutoff:3.500A) 251 hydrogen bonds defined for protein. 744 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: 0.34 Time building geometry restraints manager: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 566 1.29 - 1.42: 1080 1.42 - 1.55: 2197 1.55 - 1.68: 3 1.68 - 1.81: 34 Bond restraints: 3880 Sorted by residual: bond pdb=" C TRP A 62 " pdb=" O TRP A 62 " ideal model delta sigma weight residual 1.237 1.158 0.079 1.16e-02 7.43e+03 4.63e+01 bond pdb=" CA TRP A 62 " pdb=" CB TRP A 62 " ideal model delta sigma weight residual 1.529 1.444 0.085 1.58e-02 4.01e+03 2.87e+01 bond pdb=" CA TRP A 62 " pdb=" C TRP A 62 " ideal model delta sigma weight residual 1.524 1.467 0.057 1.26e-02 6.30e+03 2.02e+01 bond pdb=" N TRP A 62 " pdb=" CA TRP A 62 " ideal model delta sigma weight residual 1.459 1.416 0.043 1.20e-02 6.94e+03 1.31e+01 bond pdb=" C THR A 61 " pdb=" N TRP A 62 " ideal model delta sigma weight residual 1.334 1.290 0.044 1.33e-02 5.65e+03 1.09e+01 ... (remaining 3875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.16: 5240 4.16 - 8.32: 57 8.32 - 12.48: 3 12.48 - 16.64: 0 16.64 - 20.81: 2 Bond angle restraints: 5302 Sorted by residual: angle pdb=" N ALA A 222 " pdb=" CA ALA A 222 " pdb=" C ALA A 222 " ideal model delta sigma weight residual 110.91 131.72 -20.81 1.17e+00 7.31e-01 3.16e+02 angle pdb=" N GLY A 123 " pdb=" CA GLY A 123 " pdb=" C GLY A 123 " ideal model delta sigma weight residual 111.73 93.88 17.85 1.73e+00 3.34e-01 1.06e+02 angle pdb=" N SER A 367 " pdb=" CA SER A 367 " pdb=" C SER A 367 " ideal model delta sigma weight residual 110.97 118.10 -7.13 1.09e+00 8.42e-01 4.28e+01 angle pdb=" C ALA A 222 " pdb=" CA ALA A 222 " pdb=" CB ALA A 222 " ideal model delta sigma weight residual 112.27 100.85 11.42 1.75e+00 3.27e-01 4.26e+01 angle pdb=" CA THR A 61 " pdb=" C THR A 61 " pdb=" N TRP A 62 " ideal model delta sigma weight residual 117.30 123.91 -6.61 1.16e+00 7.43e-01 3.25e+01 ... (remaining 5297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.80: 2086 21.80 - 43.59: 126 43.59 - 65.39: 10 65.39 - 87.19: 10 87.19 - 108.98: 4 Dihedral angle restraints: 2236 sinusoidal: 820 harmonic: 1416 Sorted by residual: dihedral pdb=" CA VAL A 203 " pdb=" C VAL A 203 " pdb=" N PRO A 204 " pdb=" CA PRO A 204 " ideal model delta harmonic sigma weight residual 180.00 152.24 27.76 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA LYS A 428 " pdb=" C LYS A 428 " pdb=" N GLY A 429 " pdb=" CA GLY A 429 " ideal model delta harmonic sigma weight residual 180.00 156.03 23.97 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA TYR A 364 " pdb=" C TYR A 364 " pdb=" N GLN A 365 " pdb=" CA GLN A 365 " ideal model delta harmonic sigma weight residual 180.00 157.37 22.63 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 2233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 596 0.102 - 0.205: 25 0.205 - 0.307: 3 0.307 - 0.410: 0 0.410 - 0.512: 2 Chirality restraints: 626 Sorted by residual: chirality pdb=" CA ALA A 222 " pdb=" N ALA A 222 " pdb=" C ALA A 222 " pdb=" CB ALA A 222 " both_signs ideal model delta sigma weight residual False 2.48 1.97 0.51 2.00e-01 2.50e+01 6.56e+00 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 301 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.12e+00 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 623 not shown) Planarity restraints: 643 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 221 " 0.016 2.00e-02 2.50e+03 3.15e-02 9.92e+00 pdb=" C HIS A 221 " -0.054 2.00e-02 2.50e+03 pdb=" O HIS A 221 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA A 222 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 377 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.95e+00 pdb=" C ILE A 377 " 0.034 2.00e-02 2.50e+03 pdb=" O ILE A 377 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL A 378 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 314 " 0.010 2.00e-02 2.50e+03 1.89e-02 3.59e+00 pdb=" C GLU A 314 " -0.033 2.00e-02 2.50e+03 pdb=" O GLU A 314 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU A 315 " 0.011 2.00e-02 2.50e+03 ... (remaining 640 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 92 2.70 - 3.25: 3949 3.25 - 3.80: 5988 3.80 - 4.35: 7159 4.35 - 4.90: 12071 Nonbonded interactions: 29259 Sorted by model distance: nonbonded pdb=" NH1 ARG A 369 " pdb=" O GLN A 370 " model vdw 2.149 3.120 nonbonded pdb=" OH TYR A 91 " pdb=" OG SER A 410 " model vdw 2.235 3.040 nonbonded pdb=" OD1 ASP A 188 " pdb=" OE1 GLN A 191 " model vdw 2.244 3.040 nonbonded pdb=" O ALA A 343 " pdb=" OG SER A 346 " model vdw 2.269 3.040 nonbonded pdb=" NH1 ARG A 125 " pdb=" O LEU A 366 " model vdw 2.296 3.120 ... (remaining 29254 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.810 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: 0.010 Load rotamer database and sin/cos tables:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 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 0.085 3883 Z= 0.321 Angle : 1.054 20.805 5311 Z= 0.620 Chirality : 0.057 0.512 626 Planarity : 0.005 0.047 642 Dihedral : 15.385 108.985 1338 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.27 % Allowed : 0.00 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.39), residues: 487 helix: 0.90 (0.30), residues: 313 sheet: None (None), residues: 0 loop : -3.56 (0.42), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 369 TYR 0.019 0.002 TYR A 67 PHE 0.014 0.002 PHE A 14 TRP 0.018 0.002 TRP A 62 HIS 0.006 0.002 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00584 ( 3880) covalent geometry : angle 1.02921 ( 5302) hydrogen bonds : bond 0.14458 ( 251) hydrogen bonds : angle 6.80963 ( 744) link_BETA1-4 : bond 0.00389 ( 2) link_BETA1-4 : angle 3.56125 ( 6) link_NAG-ASN : bond 0.01739 ( 1) link_NAG-ASN : angle 8.22372 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.128 Fit side-chains REVERT: A 284 MET cc_start: 0.7773 (tpp) cc_final: 0.7381 (tpt) REVERT: A 403 TYR cc_start: 0.8519 (t80) cc_final: 0.8116 (t80) REVERT: A 484 MET cc_start: 0.8101 (tmm) cc_final: 0.7529 (ttt) outliers start: 1 outliers final: 1 residues processed: 65 average time/residue: 0.0480 time to fit residues: 4.0527 Evaluate side-chains 57 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.0570 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.175023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.156315 restraints weight = 4483.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.158474 restraints weight = 3164.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.159942 restraints weight = 2456.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.161072 restraints weight = 2049.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.161472 restraints weight = 1818.520| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3883 Z= 0.157 Angle : 0.758 11.119 5311 Z= 0.375 Chirality : 0.044 0.319 626 Planarity : 0.005 0.041 642 Dihedral : 9.305 65.234 592 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.21 % Favored : 91.58 % Rotamer: Outliers : 1.33 % Allowed : 9.02 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.40), residues: 487 helix: 1.38 (0.30), residues: 314 sheet: -1.59 (1.55), residues: 10 loop : -3.75 (0.43), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 28 TYR 0.017 0.002 TYR A 111 PHE 0.016 0.002 PHE A 244 TRP 0.011 0.001 TRP A 254 HIS 0.007 0.002 HIS A 221 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 3880) covalent geometry : angle 0.72471 ( 5302) hydrogen bonds : bond 0.04984 ( 251) hydrogen bonds : angle 5.52757 ( 744) link_BETA1-4 : bond 0.00506 ( 2) link_BETA1-4 : angle 3.64601 ( 6) link_NAG-ASN : bond 0.01539 ( 1) link_NAG-ASN : angle 7.86075 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.083 Fit side-chains REVERT: A 76 TYR cc_start: 0.8670 (t80) cc_final: 0.8311 (t80) REVERT: A 161 MET cc_start: 0.6570 (tmm) cc_final: 0.5642 (tpt) REVERT: A 242 ASP cc_start: 0.7903 (t70) cc_final: 0.7643 (t0) outliers start: 5 outliers final: 3 residues processed: 59 average time/residue: 0.0489 time to fit residues: 3.7412 Evaluate side-chains 51 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 345 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 21 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 28 optimal weight: 0.0870 chunk 40 optimal weight: 2.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.172999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.154980 restraints weight = 4510.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.157104 restraints weight = 3180.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.158366 restraints weight = 2471.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.159635 restraints weight = 2094.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.159636 restraints weight = 1845.950| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3883 Z= 0.166 Angle : 0.735 10.517 5311 Z= 0.364 Chirality : 0.044 0.325 626 Planarity : 0.004 0.043 642 Dihedral : 7.392 56.988 592 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 1.33 % Allowed : 14.85 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.40), residues: 487 helix: 1.50 (0.30), residues: 314 sheet: -1.79 (1.53), residues: 10 loop : -3.60 (0.46), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 446 TYR 0.013 0.001 TYR A 364 PHE 0.025 0.002 PHE A 386 TRP 0.011 0.001 TRP A 254 HIS 0.003 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 3880) covalent geometry : angle 0.70468 ( 5302) hydrogen bonds : bond 0.04794 ( 251) hydrogen bonds : angle 5.34363 ( 744) link_BETA1-4 : bond 0.00501 ( 2) link_BETA1-4 : angle 3.38797 ( 6) link_NAG-ASN : bond 0.01545 ( 1) link_NAG-ASN : angle 7.48435 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.138 Fit side-chains REVERT: A 76 TYR cc_start: 0.8700 (t80) cc_final: 0.8421 (t80) REVERT: A 106 MET cc_start: 0.8343 (tpt) cc_final: 0.7900 (tpt) REVERT: A 119 GLN cc_start: 0.8022 (mt0) cc_final: 0.7719 (mp10) REVERT: A 161 MET cc_start: 0.6573 (tmm) cc_final: 0.5663 (tpt) outliers start: 5 outliers final: 5 residues processed: 56 average time/residue: 0.0488 time to fit residues: 3.4961 Evaluate side-chains 53 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 346 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 0.7980 chunk 40 optimal weight: 0.0170 chunk 41 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 30 optimal weight: 0.0970 chunk 23 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.177058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.158791 restraints weight = 4481.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.161049 restraints weight = 3113.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.162547 restraints weight = 2407.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.163823 restraints weight = 1997.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.164495 restraints weight = 1741.311| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3883 Z= 0.134 Angle : 0.689 10.179 5311 Z= 0.340 Chirality : 0.042 0.316 626 Planarity : 0.004 0.040 642 Dihedral : 6.929 59.111 592 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 2.12 % Allowed : 17.77 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.41), residues: 487 helix: 1.66 (0.30), residues: 315 sheet: -1.49 (1.64), residues: 10 loop : -3.49 (0.46), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 446 TYR 0.019 0.001 TYR A 111 PHE 0.019 0.001 PHE A 386 TRP 0.012 0.001 TRP A 406 HIS 0.003 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 3880) covalent geometry : angle 0.65958 ( 5302) hydrogen bonds : bond 0.04151 ( 251) hydrogen bonds : angle 5.13878 ( 744) link_BETA1-4 : bond 0.00540 ( 2) link_BETA1-4 : angle 3.16572 ( 6) link_NAG-ASN : bond 0.01503 ( 1) link_NAG-ASN : angle 7.24058 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.105 Fit side-chains REVERT: A 76 TYR cc_start: 0.8655 (t80) cc_final: 0.8446 (t80) REVERT: A 106 MET cc_start: 0.8249 (tpt) cc_final: 0.7899 (tpt) REVERT: A 161 MET cc_start: 0.6482 (tmm) cc_final: 0.6017 (tpp) outliers start: 8 outliers final: 5 residues processed: 56 average time/residue: 0.0472 time to fit residues: 3.4455 Evaluate side-chains 51 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 411 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.176504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.158204 restraints weight = 4484.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.160186 restraints weight = 3149.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.161930 restraints weight = 2467.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.162859 restraints weight = 2070.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.163702 restraints weight = 1829.192| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3883 Z= 0.145 Angle : 0.693 10.034 5311 Z= 0.342 Chirality : 0.042 0.323 626 Planarity : 0.004 0.040 642 Dihedral : 6.806 58.501 592 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 2.92 % Allowed : 17.51 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.41), residues: 487 helix: 1.69 (0.30), residues: 313 sheet: -1.53 (1.65), residues: 10 loop : -3.43 (0.47), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 446 TYR 0.017 0.001 TYR A 111 PHE 0.017 0.001 PHE A 386 TRP 0.012 0.001 TRP A 27 HIS 0.002 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 3880) covalent geometry : angle 0.66449 ( 5302) hydrogen bonds : bond 0.04297 ( 251) hydrogen bonds : angle 5.07946 ( 744) link_BETA1-4 : bond 0.00538 ( 2) link_BETA1-4 : angle 3.00920 ( 6) link_NAG-ASN : bond 0.01494 ( 1) link_NAG-ASN : angle 7.15549 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.121 Fit side-chains REVERT: A 62 TRP cc_start: 0.8314 (OUTLIER) cc_final: 0.7041 (m-90) REVERT: A 76 TYR cc_start: 0.8647 (t80) cc_final: 0.8431 (t80) REVERT: A 161 MET cc_start: 0.6441 (tmm) cc_final: 0.5484 (tpt) outliers start: 11 outliers final: 8 residues processed: 53 average time/residue: 0.0453 time to fit residues: 3.2405 Evaluate side-chains 54 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 46 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 0.0570 chunk 12 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 29 optimal weight: 0.1980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** 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 = 0.3837 r_free = 0.3837 target = 0.178635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.160076 restraints weight = 4485.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.162087 restraints weight = 3135.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.163923 restraints weight = 2442.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.165026 restraints weight = 2025.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.165590 restraints weight = 1774.972| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3883 Z= 0.133 Angle : 0.671 9.684 5311 Z= 0.332 Chirality : 0.041 0.316 626 Planarity : 0.004 0.038 642 Dihedral : 6.602 55.929 592 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 3.45 % Allowed : 18.57 % Favored : 77.98 % 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 aren not related in a simple way. whole: 0.15 (0.41), residues: 487 helix: 1.75 (0.30), residues: 315 sheet: -1.48 (1.68), residues: 10 loop : -3.36 (0.48), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 446 TYR 0.016 0.001 TYR A 111 PHE 0.015 0.001 PHE A 386 TRP 0.012 0.001 TRP A 406 HIS 0.001 0.001 HIS A 221 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 3880) covalent geometry : angle 0.64358 ( 5302) hydrogen bonds : bond 0.04018 ( 251) hydrogen bonds : angle 4.99612 ( 744) link_BETA1-4 : bond 0.00517 ( 2) link_BETA1-4 : angle 2.93628 ( 6) link_NAG-ASN : bond 0.01501 ( 1) link_NAG-ASN : angle 6.90667 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.131 Fit side-chains REVERT: A 62 TRP cc_start: 0.8263 (OUTLIER) cc_final: 0.7311 (m-90) REVERT: A 161 MET cc_start: 0.6294 (tmm) cc_final: 0.5699 (tpt) outliers start: 13 outliers final: 9 residues processed: 52 average time/residue: 0.0427 time to fit residues: 3.1422 Evaluate side-chains 51 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 443 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 2 optimal weight: 0.5980 chunk 21 optimal weight: 0.0670 chunk 5 optimal weight: 0.1980 chunk 31 optimal weight: 3.9990 chunk 33 optimal weight: 0.0670 chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 chunk 14 optimal weight: 0.5980 chunk 34 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 overall best weight: 0.2856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.181454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.162906 restraints weight = 4524.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.165268 restraints weight = 3114.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.166991 restraints weight = 2378.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.167889 restraints weight = 1974.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.168738 restraints weight = 1747.782| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3883 Z= 0.125 Angle : 0.659 9.556 5311 Z= 0.324 Chirality : 0.041 0.314 626 Planarity : 0.004 0.036 642 Dihedral : 6.417 56.199 592 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 3.18 % Allowed : 18.83 % Favored : 77.98 % 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 aren not related in a simple way. whole: 0.32 (0.41), residues: 487 helix: 1.96 (0.30), residues: 310 sheet: -1.40 (1.72), residues: 10 loop : -3.33 (0.48), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 446 TYR 0.014 0.001 TYR A 111 PHE 0.011 0.001 PHE A 386 TRP 0.012 0.001 TRP A 406 HIS 0.001 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 3880) covalent geometry : angle 0.63250 ( 5302) hydrogen bonds : bond 0.03796 ( 251) hydrogen bonds : angle 4.90241 ( 744) link_BETA1-4 : bond 0.00546 ( 2) link_BETA1-4 : angle 2.84253 ( 6) link_NAG-ASN : bond 0.01444 ( 1) link_NAG-ASN : angle 6.72516 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.110 Fit side-chains REVERT: A 62 TRP cc_start: 0.8178 (OUTLIER) cc_final: 0.7287 (m-90) REVERT: A 161 MET cc_start: 0.6261 (tmm) cc_final: 0.5592 (tpt) REVERT: A 207 LEU cc_start: 0.6202 (OUTLIER) cc_final: 0.5542 (pt) outliers start: 12 outliers final: 7 residues processed: 55 average time/residue: 0.0449 time to fit residues: 3.4558 Evaluate side-chains 51 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 443 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 17 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.177632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.158870 restraints weight = 4467.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.161137 restraints weight = 3126.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.162795 restraints weight = 2404.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.163975 restraints weight = 1993.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.164395 restraints weight = 1743.143| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3883 Z= 0.145 Angle : 0.670 9.540 5311 Z= 0.331 Chirality : 0.041 0.324 626 Planarity : 0.004 0.037 642 Dihedral : 6.398 55.944 592 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 3.45 % Allowed : 18.83 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.41), residues: 487 helix: 2.04 (0.30), residues: 308 sheet: -1.52 (1.71), residues: 10 loop : -3.38 (0.47), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 446 TYR 0.013 0.001 TYR A 111 PHE 0.015 0.001 PHE A 386 TRP 0.013 0.001 TRP A 406 HIS 0.002 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 3880) covalent geometry : angle 0.64462 ( 5302) hydrogen bonds : bond 0.04201 ( 251) hydrogen bonds : angle 4.94533 ( 744) link_BETA1-4 : bond 0.00545 ( 2) link_BETA1-4 : angle 2.74524 ( 6) link_NAG-ASN : bond 0.01509 ( 1) link_NAG-ASN : angle 6.77372 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.083 Fit side-chains REVERT: A 62 TRP cc_start: 0.8283 (OUTLIER) cc_final: 0.7385 (m-90) REVERT: A 161 MET cc_start: 0.6335 (tmm) cc_final: 0.5709 (tpt) REVERT: A 207 LEU cc_start: 0.6421 (OUTLIER) cc_final: 0.5763 (pt) outliers start: 13 outliers final: 9 residues processed: 50 average time/residue: 0.0413 time to fit residues: 2.8800 Evaluate side-chains 51 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 443 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 33 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 44 optimal weight: 0.0970 chunk 18 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.179124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.160355 restraints weight = 4471.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.162537 restraints weight = 3095.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.164430 restraints weight = 2393.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.165467 restraints weight = 1978.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.165790 restraints weight = 1740.149| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3883 Z= 0.132 Angle : 0.666 9.526 5311 Z= 0.327 Chirality : 0.041 0.317 626 Planarity : 0.004 0.037 642 Dihedral : 6.327 56.141 592 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.39 % Allowed : 20.16 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.42), residues: 487 helix: 2.06 (0.31), residues: 310 sheet: -1.35 (1.75), residues: 10 loop : -3.36 (0.47), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 446 TYR 0.012 0.001 TYR A 111 PHE 0.013 0.001 PHE A 244 TRP 0.014 0.001 TRP A 406 HIS 0.001 0.001 HIS A 221 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 3880) covalent geometry : angle 0.64047 ( 5302) hydrogen bonds : bond 0.04006 ( 251) hydrogen bonds : angle 4.90804 ( 744) link_BETA1-4 : bond 0.00549 ( 2) link_BETA1-4 : angle 2.77491 ( 6) link_NAG-ASN : bond 0.01491 ( 1) link_NAG-ASN : angle 6.64756 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.102 Fit side-chains REVERT: A 62 TRP cc_start: 0.8225 (OUTLIER) cc_final: 0.7339 (m-90) REVERT: A 161 MET cc_start: 0.6281 (tmm) cc_final: 0.5579 (tpt) REVERT: A 207 LEU cc_start: 0.6184 (OUTLIER) cc_final: 0.5502 (pt) outliers start: 9 outliers final: 7 residues processed: 51 average time/residue: 0.0574 time to fit residues: 3.9029 Evaluate side-chains 52 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 443 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 38 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.178861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.160011 restraints weight = 4527.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.162373 restraints weight = 3128.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.163798 restraints weight = 2410.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.165194 restraints weight = 2019.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.165350 restraints weight = 1764.966| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3883 Z= 0.136 Angle : 0.671 9.528 5311 Z= 0.327 Chirality : 0.041 0.322 626 Planarity : 0.004 0.037 642 Dihedral : 6.288 56.071 592 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 2.92 % Allowed : 19.89 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.41), residues: 487 helix: 2.04 (0.30), residues: 310 sheet: -1.32 (1.78), residues: 10 loop : -3.33 (0.47), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 446 TYR 0.012 0.001 TYR A 111 PHE 0.014 0.001 PHE A 386 TRP 0.014 0.001 TRP A 406 HIS 0.001 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 3880) covalent geometry : angle 0.64594 ( 5302) hydrogen bonds : bond 0.04080 ( 251) hydrogen bonds : angle 4.90804 ( 744) link_BETA1-4 : bond 0.00565 ( 2) link_BETA1-4 : angle 2.72108 ( 6) link_NAG-ASN : bond 0.01464 ( 1) link_NAG-ASN : angle 6.65259 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.095 Fit side-chains REVERT: A 62 TRP cc_start: 0.8224 (OUTLIER) cc_final: 0.7380 (m-90) REVERT: A 161 MET cc_start: 0.6321 (tmm) cc_final: 0.5653 (tpt) REVERT: A 207 LEU cc_start: 0.6275 (OUTLIER) cc_final: 0.5571 (pt) outliers start: 11 outliers final: 8 residues processed: 52 average time/residue: 0.0480 time to fit residues: 3.3088 Evaluate side-chains 53 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 411 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 15 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.177487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.158562 restraints weight = 4466.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.160905 restraints weight = 3126.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.162303 restraints weight = 2423.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.163690 restraints weight = 2041.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.164385 restraints weight = 1772.721| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3883 Z= 0.144 Angle : 0.677 9.508 5311 Z= 0.332 Chirality : 0.041 0.323 626 Planarity : 0.004 0.037 642 Dihedral : 6.301 55.980 592 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 3.18 % Allowed : 19.36 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.42), residues: 487 helix: 2.04 (0.30), residues: 310 sheet: -1.31 (1.77), residues: 10 loop : -3.37 (0.47), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 446 TYR 0.012 0.001 TYR A 111 PHE 0.014 0.001 PHE A 386 TRP 0.014 0.001 TRP A 406 HIS 0.001 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 3880) covalent geometry : angle 0.65228 ( 5302) hydrogen bonds : bond 0.04209 ( 251) hydrogen bonds : angle 4.93189 ( 744) link_BETA1-4 : bond 0.00573 ( 2) link_BETA1-4 : angle 2.70415 ( 6) link_NAG-ASN : bond 0.01490 ( 1) link_NAG-ASN : angle 6.62159 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 679.69 seconds wall clock time: 12 minutes 21.32 seconds (741.32 seconds total)