Starting phenix.real_space_refine on Wed Sep 17 04:55:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jda_61386/09_2025/9jda_61386_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jda_61386/09_2025/9jda_61386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jda_61386/09_2025/9jda_61386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jda_61386/09_2025/9jda_61386.map" model { file = "/net/cci-nas-00/data/ceres_data/9jda_61386/09_2025/9jda_61386_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jda_61386/09_2025/9jda_61386_neut.cif" } resolution = 3.23 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= 0.039 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: 6 Type Number sf(0) Gaussians S 33 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 2963 2.51 5 N 668 2.21 5 O 750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4417 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4369 Classifications: {'peptide': 552} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 28, 'TRANS': 523} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 48 Unusual residues: {' CL': 1, ' NA': 2, 'D10': 1, 'D12': 1, 'OCT': 2, 'TAU': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 1.42, per 1000 atoms: 0.32 Number of scatterers: 4417 At special positions: 0 Unit cell: (83.345, 67.52, 89.675, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 33 16.00 Na 2 11.00 O 750 8.00 N 668 7.00 C 2963 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 234.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1006 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 1 sheets defined 75.9% alpha, 0.4% 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 46 through 59 removed outlier: 3.524A pdb=" N PHE A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.841A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 79 through 106 removed outlier: 6.060A pdb=" N LEU A 92 " --> pdb=" O PHE A 88 " (cutoff:3.500A) Proline residue: A 93 - end of helix Processing helix chain 'A' and resid 110 through 117 Processing helix chain 'A' and resid 121 through 152 removed outlier: 4.141A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 217 through 236 Processing helix chain 'A' and resid 241 through 244 removed outlier: 4.427A pdb=" N LYS A 244 " --> pdb=" O SER A 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 241 through 244' Processing helix chain 'A' and resid 245 through 266 Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.607A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 removed outlier: 3.503A pdb=" N GLU A 286 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 302 removed outlier: 4.232A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE A 299 " --> pdb=" O GLY A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 314 Processing helix chain 'A' and resid 321 through 356 removed outlier: 4.219A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'A' and resid 369 through 381 removed outlier: 3.585A pdb=" N TYR A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Proline residue: A 375 - end of helix removed outlier: 3.721A pdb=" N THR A 379 " --> pdb=" O PRO A 375 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 416 removed outlier: 3.610A pdb=" N SER A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 445 removed outlier: 4.108A pdb=" N GLU A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.840A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 Processing helix chain 'A' and resid 484 through 497 removed outlier: 3.553A pdb=" N ASP A 490 " --> pdb=" O ASP A 486 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY A 491 " --> pdb=" O ASN A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 510 Processing helix chain 'A' and resid 510 through 526 removed outlier: 3.610A pdb=" N LEU A 524 " --> pdb=" O PHE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 555 removed outlier: 4.015A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 568 Processing helix chain 'A' and resid 571 through 580 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 277 hydrogen bonds defined for protein. 816 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: 0.73 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1092 1.33 - 1.45: 985 1.45 - 1.57: 2428 1.57 - 1.69: 0 1.69 - 1.81: 47 Bond restraints: 4552 Sorted by residual: bond pdb=" N VAL A 195 " pdb=" CA VAL A 195 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.19e-02 7.06e+03 7.71e+00 bond pdb=" N ILE A 196 " pdb=" CA ILE A 196 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.25e+00 bond pdb=" N VAL A 590 " pdb=" CA VAL A 590 " ideal model delta sigma weight residual 1.462 1.493 -0.031 1.14e-02 7.69e+03 7.17e+00 bond pdb=" N GLU A 591 " pdb=" CA GLU A 591 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.23e-02 6.61e+03 6.16e+00 bond pdb=" N ARG A 201 " pdb=" CA ARG A 201 " ideal model delta sigma weight residual 1.456 1.487 -0.032 1.32e-02 5.74e+03 5.73e+00 ... (remaining 4547 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 6096 2.01 - 4.02: 85 4.02 - 6.03: 11 6.03 - 8.04: 1 8.04 - 10.05: 2 Bond angle restraints: 6195 Sorted by residual: angle pdb=" CA ARG A 587 " pdb=" C ARG A 587 " pdb=" O ARG A 587 " ideal model delta sigma weight residual 122.38 117.90 4.48 1.49e+00 4.50e-01 9.04e+00 angle pdb=" CA VAL A 590 " pdb=" C VAL A 590 " pdb=" O VAL A 590 " ideal model delta sigma weight residual 121.27 118.19 3.08 1.04e+00 9.25e-01 8.79e+00 angle pdb=" CA TRP A 199 " pdb=" C TRP A 199 " pdb=" O TRP A 199 " ideal model delta sigma weight residual 120.82 117.90 2.92 1.05e+00 9.07e-01 7.72e+00 angle pdb=" C VAL A 136 " pdb=" N TYR A 137 " pdb=" CA TYR A 137 " ideal model delta sigma weight residual 122.26 117.61 4.65 1.73e+00 3.34e-01 7.23e+00 angle pdb=" CA ASN A 586 " pdb=" C ASN A 586 " pdb=" O ASN A 586 " ideal model delta sigma weight residual 122.38 118.39 3.99 1.49e+00 4.50e-01 7.18e+00 ... (remaining 6190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.05: 2253 14.05 - 28.10: 237 28.10 - 42.15: 76 42.15 - 56.20: 8 56.20 - 70.25: 5 Dihedral angle restraints: 2579 sinusoidal: 991 harmonic: 1588 Sorted by residual: dihedral pdb=" CA GLU A 200 " pdb=" C GLU A 200 " pdb=" N ARG A 201 " pdb=" CA ARG A 201 " ideal model delta harmonic sigma weight residual -180.00 -157.74 -22.26 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA MET A 172 " pdb=" C MET A 172 " pdb=" N GLU A 173 " pdb=" CA GLU A 173 " ideal model delta harmonic sigma weight residual -180.00 -161.16 -18.84 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA SER A 205 " pdb=" C SER A 205 " pdb=" N LEU A 206 " pdb=" CA LEU A 206 " ideal model delta harmonic sigma weight residual -180.00 -164.99 -15.01 0 5.00e+00 4.00e-02 9.01e+00 ... (remaining 2576 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 458 0.038 - 0.077: 165 0.077 - 0.115: 47 0.115 - 0.153: 6 0.153 - 0.191: 3 Chirality restraints: 679 Sorted by residual: chirality pdb=" CA VAL A 590 " pdb=" N VAL A 590 " pdb=" C VAL A 590 " pdb=" CB VAL A 590 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.15e-01 chirality pdb=" CA ILE A 196 " pdb=" N ILE A 196 " pdb=" C ILE A 196 " pdb=" CB ILE A 196 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.27e-01 chirality pdb=" CA THR A 596 " pdb=" N THR A 596 " pdb=" C THR A 596 " pdb=" CB THR A 596 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.04e-01 ... (remaining 676 not shown) Planarity restraints: 753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 201 " -0.212 9.50e-02 1.11e+02 9.50e-02 5.53e+00 pdb=" NE ARG A 201 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 201 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 201 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 201 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 207 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO A 208 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 208 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 208 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 87 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.71e+00 pdb=" C LEU A 87 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU A 87 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE A 88 " 0.011 2.00e-02 2.50e+03 ... (remaining 750 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 68 2.68 - 3.24: 4608 3.24 - 3.79: 7117 3.79 - 4.35: 9980 4.35 - 4.90: 16163 Nonbonded interactions: 37936 Sorted by model distance: nonbonded pdb=" OH TYR A 69 " pdb=" OD2 ASP A 459 " model vdw 2.130 3.040 nonbonded pdb=" O TYR A 247 " pdb=" OG1 THR A 251 " model vdw 2.203 3.040 nonbonded pdb=" O PHE A 342 " pdb=" OG SER A 346 " model vdw 2.245 3.040 nonbonded pdb=" OG SER A 301 " pdb="NA NA A 707 " model vdw 2.249 2.470 nonbonded pdb=" O2 TAU A 701 " pdb="NA NA A 707 " model vdw 2.253 2.470 ... (remaining 37931 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 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: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.660 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 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 : 0.004 0.036 4553 Z= 0.222 Angle : 0.607 10.054 6197 Z= 0.343 Chirality : 0.043 0.191 679 Planarity : 0.006 0.095 753 Dihedral : 12.991 70.253 1570 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -0.46 (0.34), residues: 548 helix: 0.19 (0.26), residues: 377 sheet: None (None), residues: 0 loop : -1.22 (0.45), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 428 TYR 0.025 0.001 TYR A 148 PHE 0.022 0.002 PHE A 58 TRP 0.021 0.001 TRP A 236 HIS 0.006 0.002 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 4552) covalent geometry : angle 0.60686 ( 6195) SS BOND : bond 0.00504 ( 1) SS BOND : angle 1.17283 ( 2) hydrogen bonds : bond 0.22768 ( 277) hydrogen bonds : angle 8.04031 ( 816) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.168 Fit side-chains REVERT: A 191 PHE cc_start: 0.7743 (m-10) cc_final: 0.7420 (m-80) REVERT: A 287 ASP cc_start: 0.8628 (t0) cc_final: 0.8326 (t0) REVERT: A 289 GLN cc_start: 0.7982 (tp40) cc_final: 0.7381 (pt0) REVERT: A 293 ASP cc_start: 0.8593 (m-30) cc_final: 0.8333 (m-30) REVERT: A 452 MET cc_start: 0.8885 (tpt) cc_final: 0.8543 (tpt) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.0711 time to fit residues: 7.9036 Evaluate side-chains 72 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.0670 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 74 ASN A 297 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.149739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.114723 restraints weight = 5576.543| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.93 r_work: 0.2984 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4553 Z= 0.155 Angle : 0.578 9.405 6197 Z= 0.296 Chirality : 0.041 0.185 679 Planarity : 0.005 0.050 753 Dihedral : 5.661 47.878 625 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.07 % Allowed : 6.65 % Favored : 92.27 % 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: 0.44 (0.35), residues: 548 helix: 0.96 (0.26), residues: 384 sheet: None (None), residues: 0 loop : -1.24 (0.45), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 575 TYR 0.015 0.002 TYR A 489 PHE 0.025 0.002 PHE A 58 TRP 0.013 0.001 TRP A 470 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 4552) covalent geometry : angle 0.57748 ( 6195) SS BOND : bond 0.00344 ( 1) SS BOND : angle 1.44403 ( 2) hydrogen bonds : bond 0.04473 ( 277) hydrogen bonds : angle 5.10366 ( 816) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: A 206 LEU cc_start: 0.8847 (tp) cc_final: 0.8573 (tp) REVERT: A 219 ASP cc_start: 0.8434 (p0) cc_final: 0.8233 (p0) REVERT: A 287 ASP cc_start: 0.8629 (t0) cc_final: 0.8397 (t0) REVERT: A 289 GLN cc_start: 0.8232 (tp40) cc_final: 0.7530 (pt0) REVERT: A 293 ASP cc_start: 0.8613 (m-30) cc_final: 0.8303 (m-30) REVERT: A 351 MET cc_start: 0.8840 (mtp) cc_final: 0.8300 (mtp) REVERT: A 421 PHE cc_start: 0.7834 (t80) cc_final: 0.7582 (t80) REVERT: A 452 MET cc_start: 0.8941 (tpt) cc_final: 0.8504 (tpt) REVERT: A 563 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8445 (mp) outliers start: 5 outliers final: 4 residues processed: 80 average time/residue: 0.0611 time to fit residues: 6.5446 Evaluate side-chains 69 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 563 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 36 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 16 optimal weight: 0.0030 chunk 25 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN A 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.152276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.117623 restraints weight = 5551.750| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.94 r_work: 0.2987 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4553 Z= 0.148 Angle : 0.553 9.153 6197 Z= 0.279 Chirality : 0.041 0.193 679 Planarity : 0.004 0.052 753 Dihedral : 5.484 41.616 625 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.72 % Allowed : 8.58 % Favored : 89.70 % 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: 0.63 (0.35), residues: 548 helix: 1.14 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -1.30 (0.44), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 575 TYR 0.022 0.001 TYR A 489 PHE 0.029 0.002 PHE A 58 TRP 0.011 0.001 TRP A 470 HIS 0.001 0.000 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 4552) covalent geometry : angle 0.55295 ( 6195) SS BOND : bond 0.00366 ( 1) SS BOND : angle 1.14732 ( 2) hydrogen bonds : bond 0.03997 ( 277) hydrogen bonds : angle 4.78518 ( 816) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: A 206 LEU cc_start: 0.8848 (tp) cc_final: 0.8590 (tp) REVERT: A 289 GLN cc_start: 0.8289 (tp40) cc_final: 0.7478 (tt0) REVERT: A 293 ASP cc_start: 0.8642 (m-30) cc_final: 0.8335 (m-30) REVERT: A 421 PHE cc_start: 0.7912 (t80) cc_final: 0.7584 (t80) REVERT: A 452 MET cc_start: 0.9032 (tpt) cc_final: 0.8598 (tpt) REVERT: A 596 THR cc_start: 0.7221 (OUTLIER) cc_final: 0.6860 (m) outliers start: 8 outliers final: 5 residues processed: 81 average time/residue: 0.0642 time to fit residues: 6.7730 Evaluate side-chains 72 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 48 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 13 optimal weight: 0.1980 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 3 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.149493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.115180 restraints weight = 5573.287| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.89 r_work: 0.2990 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4553 Z= 0.143 Angle : 0.532 9.340 6197 Z= 0.270 Chirality : 0.040 0.187 679 Planarity : 0.004 0.053 753 Dihedral : 5.279 41.189 625 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.50 % Allowed : 10.94 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.35), residues: 548 helix: 1.30 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -1.29 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 583 TYR 0.018 0.001 TYR A 489 PHE 0.029 0.002 PHE A 58 TRP 0.011 0.001 TRP A 470 HIS 0.001 0.000 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 4552) covalent geometry : angle 0.53120 ( 6195) SS BOND : bond 0.00330 ( 1) SS BOND : angle 1.21512 ( 2) hydrogen bonds : bond 0.03762 ( 277) hydrogen bonds : angle 4.67679 ( 816) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: A 289 GLN cc_start: 0.8411 (tp40) cc_final: 0.7506 (tt0) REVERT: A 293 ASP cc_start: 0.8664 (m-30) cc_final: 0.8364 (m-30) REVERT: A 421 PHE cc_start: 0.7938 (t80) cc_final: 0.7558 (t80) REVERT: A 452 MET cc_start: 0.9074 (tpt) cc_final: 0.8642 (tpt) REVERT: A 596 THR cc_start: 0.7269 (OUTLIER) cc_final: 0.6943 (m) outliers start: 7 outliers final: 6 residues processed: 77 average time/residue: 0.0546 time to fit residues: 5.7183 Evaluate side-chains 72 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 6 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 54 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN A 212 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.152334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.117411 restraints weight = 5525.488| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.95 r_work: 0.2998 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4553 Z= 0.140 Angle : 0.540 9.270 6197 Z= 0.271 Chirality : 0.040 0.187 679 Planarity : 0.004 0.053 753 Dihedral : 5.171 40.345 625 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.36 % Allowed : 10.30 % Favored : 87.34 % 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: 0.92 (0.35), residues: 548 helix: 1.38 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -1.23 (0.44), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 428 TYR 0.016 0.001 TYR A 69 PHE 0.028 0.002 PHE A 58 TRP 0.010 0.001 TRP A 470 HIS 0.005 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 4552) covalent geometry : angle 0.53963 ( 6195) SS BOND : bond 0.00273 ( 1) SS BOND : angle 1.00826 ( 2) hydrogen bonds : bond 0.03707 ( 277) hydrogen bonds : angle 4.61260 ( 816) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.9384 (OUTLIER) cc_final: 0.8359 (p90) REVERT: A 206 LEU cc_start: 0.8800 (tp) cc_final: 0.8523 (tp) REVERT: A 289 GLN cc_start: 0.8346 (tp40) cc_final: 0.7519 (pt0) REVERT: A 293 ASP cc_start: 0.8603 (m-30) cc_final: 0.8306 (m-30) REVERT: A 421 PHE cc_start: 0.7923 (t80) cc_final: 0.7553 (t80) REVERT: A 429 GLU cc_start: 0.8090 (mp0) cc_final: 0.7731 (pm20) REVERT: A 452 MET cc_start: 0.9094 (tpt) cc_final: 0.8689 (tpt) REVERT: A 564 ARG cc_start: 0.8374 (mmt90) cc_final: 0.8130 (mmt180) REVERT: A 596 THR cc_start: 0.7227 (OUTLIER) cc_final: 0.7007 (m) outliers start: 11 outliers final: 7 residues processed: 82 average time/residue: 0.0596 time to fit residues: 6.5454 Evaluate side-chains 77 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 48 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 47 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.150623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.115834 restraints weight = 5699.889| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.95 r_work: 0.2996 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4553 Z= 0.151 Angle : 0.552 9.299 6197 Z= 0.277 Chirality : 0.040 0.185 679 Planarity : 0.004 0.051 753 Dihedral : 5.160 39.851 625 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.93 % Allowed : 12.02 % Favored : 86.05 % 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: 0.92 (0.35), residues: 548 helix: 1.39 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -1.26 (0.44), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 66 TYR 0.017 0.001 TYR A 69 PHE 0.028 0.002 PHE A 58 TRP 0.010 0.001 TRP A 470 HIS 0.006 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 4552) covalent geometry : angle 0.55196 ( 6195) SS BOND : bond 0.00319 ( 1) SS BOND : angle 0.87651 ( 2) hydrogen bonds : bond 0.03716 ( 277) hydrogen bonds : angle 4.63055 ( 816) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.157 Fit side-chains REVERT: A 69 TYR cc_start: 0.9380 (OUTLIER) cc_final: 0.8425 (p90) REVERT: A 125 TYR cc_start: 0.9091 (m-80) cc_final: 0.8709 (m-80) REVERT: A 191 PHE cc_start: 0.7922 (m-10) cc_final: 0.7611 (m-10) REVERT: A 206 LEU cc_start: 0.8849 (tp) cc_final: 0.8552 (tp) REVERT: A 289 GLN cc_start: 0.8368 (tp40) cc_final: 0.7502 (pt0) REVERT: A 293 ASP cc_start: 0.8615 (m-30) cc_final: 0.8324 (m-30) REVERT: A 421 PHE cc_start: 0.7969 (t80) cc_final: 0.7588 (t80) REVERT: A 429 GLU cc_start: 0.8190 (mp0) cc_final: 0.7804 (pm20) REVERT: A 452 MET cc_start: 0.9112 (tpt) cc_final: 0.8693 (tpt) REVERT: A 596 THR cc_start: 0.7354 (OUTLIER) cc_final: 0.7018 (m) outliers start: 9 outliers final: 6 residues processed: 79 average time/residue: 0.0581 time to fit residues: 6.2126 Evaluate side-chains 76 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 49 optimal weight: 0.2980 chunk 48 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.151703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.116920 restraints weight = 5635.597| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.94 r_work: 0.3000 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4553 Z= 0.141 Angle : 0.544 9.284 6197 Z= 0.273 Chirality : 0.040 0.188 679 Planarity : 0.004 0.052 753 Dihedral : 5.098 38.424 625 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.15 % Allowed : 11.80 % Favored : 86.05 % 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: 0.98 (0.35), residues: 548 helix: 1.45 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -1.28 (0.44), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.017 0.001 TYR A 69 PHE 0.028 0.002 PHE A 58 TRP 0.010 0.001 TRP A 470 HIS 0.008 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 4552) covalent geometry : angle 0.54387 ( 6195) SS BOND : bond 0.00265 ( 1) SS BOND : angle 0.94338 ( 2) hydrogen bonds : bond 0.03656 ( 277) hydrogen bonds : angle 4.57634 ( 816) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.164 Fit side-chains REVERT: A 69 TYR cc_start: 0.9352 (OUTLIER) cc_final: 0.8458 (p90) REVERT: A 191 PHE cc_start: 0.7789 (m-10) cc_final: 0.7532 (m-10) REVERT: A 206 LEU cc_start: 0.8843 (tp) cc_final: 0.8609 (tp) REVERT: A 289 GLN cc_start: 0.8370 (tp40) cc_final: 0.7470 (pt0) REVERT: A 293 ASP cc_start: 0.8613 (m-30) cc_final: 0.8303 (m-30) REVERT: A 421 PHE cc_start: 0.7985 (t80) cc_final: 0.7618 (t80) REVERT: A 429 GLU cc_start: 0.8229 (mp0) cc_final: 0.7942 (pm20) REVERT: A 452 MET cc_start: 0.9121 (tpt) cc_final: 0.8743 (tpt) REVERT: A 596 THR cc_start: 0.7378 (OUTLIER) cc_final: 0.7052 (m) outliers start: 10 outliers final: 7 residues processed: 80 average time/residue: 0.0541 time to fit residues: 5.9908 Evaluate side-chains 79 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS A 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.151409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.116660 restraints weight = 5585.848| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.91 r_work: 0.2991 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4553 Z= 0.158 Angle : 0.570 9.975 6197 Z= 0.286 Chirality : 0.041 0.186 679 Planarity : 0.004 0.053 753 Dihedral : 5.124 38.282 625 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.58 % Allowed : 12.45 % Favored : 84.98 % 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: 0.97 (0.35), residues: 548 helix: 1.44 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -1.27 (0.44), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 66 TYR 0.018 0.002 TYR A 69 PHE 0.029 0.002 PHE A 58 TRP 0.010 0.001 TRP A 470 HIS 0.006 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 4552) covalent geometry : angle 0.56983 ( 6195) SS BOND : bond 0.00273 ( 1) SS BOND : angle 1.14269 ( 2) hydrogen bonds : bond 0.03694 ( 277) hydrogen bonds : angle 4.58990 ( 816) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.166 Fit side-chains REVERT: A 69 TYR cc_start: 0.9356 (OUTLIER) cc_final: 0.8498 (p90) REVERT: A 191 PHE cc_start: 0.7744 (m-10) cc_final: 0.7521 (m-80) REVERT: A 206 LEU cc_start: 0.8842 (tp) cc_final: 0.8605 (tp) REVERT: A 289 GLN cc_start: 0.8400 (tp40) cc_final: 0.7453 (tt0) REVERT: A 293 ASP cc_start: 0.8619 (m-30) cc_final: 0.8374 (m-30) REVERT: A 421 PHE cc_start: 0.7970 (t80) cc_final: 0.7616 (t80) REVERT: A 429 GLU cc_start: 0.8282 (mp0) cc_final: 0.7964 (pm20) REVERT: A 452 MET cc_start: 0.9136 (tpt) cc_final: 0.8693 (tpt) REVERT: A 596 THR cc_start: 0.7437 (OUTLIER) cc_final: 0.7127 (m) outliers start: 12 outliers final: 7 residues processed: 84 average time/residue: 0.0487 time to fit residues: 5.7647 Evaluate side-chains 79 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 0 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.150965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.116572 restraints weight = 5621.964| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.92 r_work: 0.2977 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4553 Z= 0.160 Angle : 0.583 11.443 6197 Z= 0.291 Chirality : 0.041 0.187 679 Planarity : 0.004 0.052 753 Dihedral : 5.163 38.207 625 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.15 % Allowed : 13.52 % Favored : 84.33 % 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 aren not related in a simple way. whole: 0.95 (0.35), residues: 548 helix: 1.43 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -1.29 (0.44), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 66 TYR 0.020 0.002 TYR A 489 PHE 0.030 0.002 PHE A 58 TRP 0.010 0.001 TRP A 470 HIS 0.008 0.002 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 4552) covalent geometry : angle 0.58276 ( 6195) SS BOND : bond 0.00241 ( 1) SS BOND : angle 1.19844 ( 2) hydrogen bonds : bond 0.03743 ( 277) hydrogen bonds : angle 4.60526 ( 816) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.177 Fit side-chains REVERT: A 69 TYR cc_start: 0.9337 (OUTLIER) cc_final: 0.8484 (p90) REVERT: A 206 LEU cc_start: 0.8843 (tp) cc_final: 0.8575 (tp) REVERT: A 289 GLN cc_start: 0.8388 (tp40) cc_final: 0.7415 (tt0) REVERT: A 293 ASP cc_start: 0.8614 (m-30) cc_final: 0.8371 (m-30) REVERT: A 421 PHE cc_start: 0.7981 (t80) cc_final: 0.7633 (t80) REVERT: A 429 GLU cc_start: 0.8269 (mp0) cc_final: 0.8062 (pm20) REVERT: A 452 MET cc_start: 0.9140 (tpt) cc_final: 0.8728 (tpt) REVERT: A 596 THR cc_start: 0.7447 (OUTLIER) cc_final: 0.7139 (m) outliers start: 10 outliers final: 7 residues processed: 80 average time/residue: 0.0487 time to fit residues: 5.4340 Evaluate side-chains 80 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 22 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 31 optimal weight: 0.0770 chunk 13 optimal weight: 0.0040 chunk 43 optimal weight: 0.4980 overall best weight: 0.3550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.153540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.119543 restraints weight = 5581.578| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.91 r_work: 0.3018 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4553 Z= 0.119 Angle : 0.567 11.215 6197 Z= 0.283 Chirality : 0.040 0.180 679 Planarity : 0.004 0.051 753 Dihedral : 4.944 33.537 625 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.93 % Allowed : 13.52 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.36), residues: 548 helix: 1.56 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -1.33 (0.44), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.017 0.001 TYR A 489 PHE 0.026 0.002 PHE A 58 TRP 0.011 0.001 TRP A 470 HIS 0.011 0.002 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 4552) covalent geometry : angle 0.56654 ( 6195) SS BOND : bond 0.00207 ( 1) SS BOND : angle 1.27027 ( 2) hydrogen bonds : bond 0.03527 ( 277) hydrogen bonds : angle 4.48544 ( 816) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.196 Fit side-chains REVERT: A 69 TYR cc_start: 0.9264 (OUTLIER) cc_final: 0.8441 (p90) REVERT: A 206 LEU cc_start: 0.8800 (tp) cc_final: 0.8554 (tp) REVERT: A 289 GLN cc_start: 0.8379 (tp40) cc_final: 0.7376 (tt0) REVERT: A 293 ASP cc_start: 0.8576 (m-30) cc_final: 0.8312 (m-30) REVERT: A 421 PHE cc_start: 0.7966 (t80) cc_final: 0.7630 (t80) REVERT: A 429 GLU cc_start: 0.8271 (mp0) cc_final: 0.8068 (pm20) REVERT: A 452 MET cc_start: 0.9112 (tpt) cc_final: 0.8775 (tpt) REVERT: A 596 THR cc_start: 0.7454 (OUTLIER) cc_final: 0.7221 (m) outliers start: 9 outliers final: 7 residues processed: 83 average time/residue: 0.0498 time to fit residues: 5.7433 Evaluate side-chains 83 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 3 optimal weight: 0.2980 chunk 17 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 14 optimal weight: 0.0870 chunk 34 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.152883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.119321 restraints weight = 5658.868| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.90 r_work: 0.3007 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4553 Z= 0.130 Angle : 0.575 9.753 6197 Z= 0.288 Chirality : 0.040 0.181 679 Planarity : 0.004 0.051 753 Dihedral : 4.904 31.880 625 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.15 % Allowed : 14.38 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.36), residues: 548 helix: 1.57 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -1.40 (0.44), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.015 0.001 TYR A 69 PHE 0.028 0.002 PHE A 58 TRP 0.010 0.001 TRP A 470 HIS 0.011 0.002 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 4552) covalent geometry : angle 0.57449 ( 6195) SS BOND : bond 0.00266 ( 1) SS BOND : angle 1.43061 ( 2) hydrogen bonds : bond 0.03539 ( 277) hydrogen bonds : angle 4.49047 ( 816) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1286.98 seconds wall clock time: 22 minutes 45.51 seconds (1365.51 seconds total)