Starting phenix.real_space_refine on Thu Jul 2 00:18:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jda_61386/07_2026/9jda_61386_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jda_61386/07_2026/9jda_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_61386/07_2026/9jda_61386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jda_61386/07_2026/9jda_61386.map" model { file = "/net/cci-nas-00/data/ceres_data/9jda_61386/07_2026/9jda_61386_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jda_61386/07_2026/9jda_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-dev-6108/lib/python3.11/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, 45 Ad-hoc single atom residues: {' CL': 1, ' NA': 2} Unusual residues: {'D10': 1, 'D12': 1, 'OCT': 2, 'TAU': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain breaks: 3 Time building chain proxies: 1.11, per 1000 atoms: 0.25 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: 0.25 Conformation dependent library (CDL) restraints added in 99.5 milliseconds 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: 0.09 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: 0.52 Time building geometry restraints manager: 0.32 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 3.210 nonbonded pdb=" O2 TAU A 701 " pdb="NA NA A 707 " model vdw 2.253 3.210 ... (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: 0.750 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.910 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 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 are 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/Z covalent geometry : bond 0.00438 / 0.22 ( 4552) covalent geometry : angle 0.60686 / 0.34 ( 6195) SS BOND : bond 0.00504 / 0.34 ( 1) SS BOND : angle 1.17283 / 0.75 ( 2) hydrogen bonds : bond 0.22768 / 15.06 ( 277) hydrogen bonds : angle 8.04031 / 5.65 ( 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 : 0.160 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: 0.0653 time to fit residues: 7.3423 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 : 0.182 ------------------------------------------------------------------------------- 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: 0.9980 chunk 16 optimal weight: 0.0670 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 ASN A 297 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.149285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.114279 restraints weight = 5584.156| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.93 r_work: 0.3001 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1424 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= 0.151 Angle : 0.580 9.398 6197 Z= 0.298 Chirality : 0.041 0.189 679 Planarity : 0.005 0.050 753 Dihedral : 5.784 47.857 625 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.07 % Allowed : 7.30 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.35), residues: 548 helix: 0.94 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -1.25 (0.46), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 575 TYR 0.013 0.001 TYR A 69 PHE 0.022 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/Z covalent geometry : bond 0.00340 / 0.15 ( 4552) covalent geometry : angle 0.58000 / 0.30 ( 6195) SS BOND : bond 0.00311 / 0.21 ( 1) SS BOND : angle 1.45745 / 0.94 ( 2) hydrogen bonds : bond 0.04310 / 2.74 ( 277) hydrogen bonds : angle 5.06917 / 3.53 ( 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 80 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: A 206 LEU cc_start: 0.8852 (tp) cc_final: 0.8578 (tp) REVERT: A 219 ASP cc_start: 0.8426 (p0) cc_final: 0.8219 (p0) REVERT: A 287 ASP cc_start: 0.8604 (t0) cc_final: 0.8363 (t0) REVERT: A 289 GLN cc_start: 0.8235 (tp40) cc_final: 0.7569 (pt0) REVERT: A 293 ASP cc_start: 0.8577 (m-30) cc_final: 0.8278 (m-30) REVERT: A 351 MET cc_start: 0.8843 (mtp) cc_final: 0.8315 (mtp) REVERT: A 421 PHE cc_start: 0.7830 (t80) cc_final: 0.7577 (t80) REVERT: A 452 MET cc_start: 0.8921 (tpt) cc_final: 0.8496 (tpt) REVERT: A 563 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8435 (mp) outliers start: 5 outliers final: 4 residues processed: 79 average time/residue: 0.0464 time to fit residues: 5.0144 Evaluate side-chains 68 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.102 ------------------------------------------------------------------------------- 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: 0.9980 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3622 r_free = 0.3622 target = 0.148046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.113183 restraints weight = 5581.215| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.93 r_work: 0.2965 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1708 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= 0.165 Angle : 0.562 9.255 6197 Z= 0.283 Chirality : 0.041 0.143 679 Planarity : 0.004 0.053 753 Dihedral : 5.869 45.875 625 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.36 % Allowed : 8.15 % Favored : 89.48 % 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 are not related in a simple way. whole: 0.59 (0.35), residues: 548 helix: 1.12 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -1.32 (0.44), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 575 TYR 0.016 0.001 TYR A 69 PHE 0.017 0.002 PHE A 350 TRP 0.011 0.001 TRP A 470 HIS 0.001 0.000 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 4552) covalent geometry : angle 0.56202 / 0.28 ( 6195) SS BOND : bond 0.00407 / 0.27 ( 1) SS BOND : angle 1.16477 / 0.72 ( 2) hydrogen bonds : bond 0.04096 / 2.61 ( 277) hydrogen bonds : angle 4.83974 / 3.39 ( 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: 11 poor density : 71 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: A 58 PHE cc_start: 0.9222 (OUTLIER) cc_final: 0.9003 (p90) REVERT: A 206 LEU cc_start: 0.8864 (tp) cc_final: 0.8599 (tp) REVERT: A 219 ASP cc_start: 0.8526 (p0) cc_final: 0.8234 (p0) REVERT: A 289 GLN cc_start: 0.8337 (tp40) cc_final: 0.7561 (tt0) REVERT: A 293 ASP cc_start: 0.8646 (m-30) cc_final: 0.8365 (m-30) REVERT: A 421 PHE cc_start: 0.7905 (t80) cc_final: 0.7569 (t80) REVERT: A 452 MET cc_start: 0.9044 (tpt) cc_final: 0.8606 (tpt) REVERT: A 596 THR cc_start: 0.7250 (OUTLIER) cc_final: 0.6887 (m) outliers start: 11 outliers final: 6 residues processed: 80 average time/residue: 0.0594 time to fit residues: 6.3050 Evaluate side-chains 73 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 48 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 24 optimal weight: 0.0980 chunk 38 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 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: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.151608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.117483 restraints weight = 5532.910| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.90 r_work: 0.2981 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1909 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= 0.154 Angle : 0.538 9.338 6197 Z= 0.271 Chirality : 0.040 0.143 679 Planarity : 0.004 0.054 753 Dihedral : 5.671 44.386 625 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.15 % Allowed : 9.87 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.35), residues: 548 helix: 1.30 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -1.22 (0.45), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 575 TYR 0.016 0.001 TYR A 69 PHE 0.012 0.002 PHE A 191 TRP 0.011 0.001 TRP A 470 HIS 0.001 0.000 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 ( 4552) covalent geometry : angle 0.53751 / 0.27 ( 6195) SS BOND : bond 0.00314 / 0.21 ( 1) SS BOND : angle 1.17279 / 0.74 ( 2) hydrogen bonds : bond 0.03809 / 2.42 ( 277) hydrogen bonds : angle 4.68736 / 3.28 ( 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 82 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: A 58 PHE cc_start: 0.9229 (OUTLIER) cc_final: 0.9011 (p90) REVERT: A 69 TYR cc_start: 0.9353 (OUTLIER) cc_final: 0.8200 (p90) REVERT: A 219 ASP cc_start: 0.8539 (p0) cc_final: 0.8205 (p0) REVERT: A 289 GLN cc_start: 0.8436 (tp40) cc_final: 0.7544 (tt0) REVERT: A 293 ASP cc_start: 0.8653 (m-30) cc_final: 0.8352 (m-30) REVERT: A 421 PHE cc_start: 0.7922 (t80) cc_final: 0.7536 (t80) REVERT: A 452 MET cc_start: 0.9086 (tpt) cc_final: 0.8659 (tpt) REVERT: A 596 THR cc_start: 0.7302 (OUTLIER) cc_final: 0.6970 (m) outliers start: 10 outliers final: 6 residues processed: 80 average time/residue: 0.0537 time to fit residues: 5.7624 Evaluate side-chains 75 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE 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=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: 2.9990 chunk 53 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 40 optimal weight: 0.4980 chunk 18 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.151576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.117061 restraints weight = 5535.329| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.91 r_work: 0.2997 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2135 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= 0.137 Angle : 0.546 9.271 6197 Z= 0.272 Chirality : 0.040 0.142 679 Planarity : 0.004 0.054 753 Dihedral : 5.439 43.379 625 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.15 % Allowed : 10.73 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.35), residues: 548 helix: 1.39 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -1.26 (0.44), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 428 TYR 0.016 0.001 TYR A 489 PHE 0.018 0.002 PHE A 350 TRP 0.011 0.001 TRP A 470 HIS 0.001 0.000 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 4552) covalent geometry : angle 0.54518 / 0.27 ( 6195) SS BOND : bond 0.00279 / 0.19 ( 1) SS BOND : angle 1.18137 / 0.77 ( 2) hydrogen bonds : bond 0.03668 / 2.33 ( 277) hydrogen bonds : angle 4.60081 / 3.23 ( 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 84 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: A 58 PHE cc_start: 0.9215 (OUTLIER) cc_final: 0.9008 (p90) REVERT: A 69 TYR cc_start: 0.9372 (OUTLIER) cc_final: 0.8314 (p90) REVERT: A 206 LEU cc_start: 0.8806 (tp) cc_final: 0.8529 (tp) REVERT: A 219 ASP cc_start: 0.8539 (p0) cc_final: 0.8204 (p0) REVERT: A 289 GLN cc_start: 0.8420 (tp40) cc_final: 0.7574 (tt0) REVERT: A 293 ASP cc_start: 0.8610 (m-30) cc_final: 0.8311 (m-30) REVERT: A 421 PHE cc_start: 0.7941 (t80) cc_final: 0.7539 (t80) REVERT: A 429 GLU cc_start: 0.8148 (mp0) cc_final: 0.7748 (pm20) REVERT: A 452 MET cc_start: 0.9086 (tpt) cc_final: 0.8667 (tpt) REVERT: A 564 ARG cc_start: 0.8344 (mmt90) cc_final: 0.8095 (mmt180) REVERT: A 596 THR cc_start: 0.7239 (OUTLIER) cc_final: 0.6889 (m) outliers start: 10 outliers final: 6 residues processed: 82 average time/residue: 0.0546 time to fit residues: 5.9747 Evaluate side-chains 78 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 161 HIS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 48 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 0.0040 chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 47 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 24 optimal weight: 0.0040 overall best weight: 0.4404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 212 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.152851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.118012 restraints weight = 5641.192| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.95 r_work: 0.3017 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2246 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= 0.119 Angle : 0.525 9.252 6197 Z= 0.263 Chirality : 0.039 0.143 679 Planarity : 0.004 0.053 753 Dihedral : 5.195 40.632 625 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.15 % Allowed : 11.16 % Favored : 86.70 % 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 are not related in a simple way. whole: 1.08 (0.36), residues: 548 helix: 1.52 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -1.25 (0.44), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.016 0.001 TYR A 489 PHE 0.023 0.001 PHE A 404 TRP 0.011 0.001 TRP A 470 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 4552) covalent geometry : angle 0.52497 / 0.26 ( 6195) SS BOND : bond 0.00354 / 0.24 ( 1) SS BOND : angle 0.83774 / 0.50 ( 2) hydrogen bonds : bond 0.03506 / 2.23 ( 277) hydrogen bonds : angle 4.51303 / 3.17 ( 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 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 58 PHE cc_start: 0.9214 (OUTLIER) cc_final: 0.9012 (p90) REVERT: A 69 TYR cc_start: 0.9351 (OUTLIER) cc_final: 0.8356 (p90) REVERT: A 125 TYR cc_start: 0.9083 (m-80) cc_final: 0.8702 (m-80) REVERT: A 191 PHE cc_start: 0.7833 (m-10) cc_final: 0.7527 (m-10) REVERT: A 206 LEU cc_start: 0.8847 (tp) cc_final: 0.8569 (tp) REVERT: A 219 ASP cc_start: 0.8547 (p0) cc_final: 0.8196 (p0) REVERT: A 289 GLN cc_start: 0.8378 (tp40) cc_final: 0.7481 (pt0) REVERT: A 293 ASP cc_start: 0.8578 (m-30) cc_final: 0.8267 (m-30) REVERT: A 351 MET cc_start: 0.8938 (mtp) cc_final: 0.8414 (mtp) REVERT: A 421 PHE cc_start: 0.7957 (t80) cc_final: 0.7572 (t80) REVERT: A 429 GLU cc_start: 0.8220 (mp0) cc_final: 0.7876 (pm20) REVERT: A 452 MET cc_start: 0.9075 (tpt) cc_final: 0.8686 (tpt) REVERT: A 564 ARG cc_start: 0.8347 (mmt90) cc_final: 0.8137 (mmt180) REVERT: A 596 THR cc_start: 0.7239 (OUTLIER) cc_final: 0.6885 (m) outliers start: 10 outliers final: 6 residues processed: 79 average time/residue: 0.0531 time to fit residues: 5.6331 Evaluate side-chains 78 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE 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 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: 2.9990 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 45 optimal weight: 0.0870 chunk 44 optimal weight: 1.9990 chunk 49 optimal weight: 0.0010 chunk 48 optimal weight: 0.0670 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 18 optimal weight: 0.6980 overall best weight: 0.2702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3688 r_free = 0.3688 target = 0.153970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.119707 restraints weight = 5601.268| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.93 r_work: 0.3035 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4553 Z= 0.105 Angle : 0.517 9.214 6197 Z= 0.258 Chirality : 0.039 0.142 679 Planarity : 0.004 0.050 753 Dihedral : 4.960 36.914 625 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.93 % Allowed : 12.23 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.36), residues: 548 helix: 1.63 (0.27), 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 0.015 0.001 TYR A 489 PHE 0.020 0.001 PHE A 350 TRP 0.011 0.001 TRP A 470 HIS 0.011 0.002 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 4552) covalent geometry : angle 0.51679 / 0.26 ( 6195) SS BOND : bond 0.00177 / 0.12 ( 1) SS BOND : angle 1.04125 / 0.66 ( 2) hydrogen bonds : bond 0.03368 / 2.15 ( 277) hydrogen bonds : angle 4.42573 / 3.11 ( 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 84 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.162 Fit side-chains REVERT: A 69 TYR cc_start: 0.9261 (OUTLIER) cc_final: 0.8289 (p90) REVERT: A 191 PHE cc_start: 0.7626 (m-10) cc_final: 0.7401 (m-10) REVERT: A 206 LEU cc_start: 0.8661 (tp) cc_final: 0.8389 (tp) REVERT: A 219 ASP cc_start: 0.8374 (p0) cc_final: 0.8043 (p0) REVERT: A 289 GLN cc_start: 0.8214 (tp40) cc_final: 0.7494 (pt0) REVERT: A 293 ASP cc_start: 0.8395 (m-30) cc_final: 0.8173 (m-30) REVERT: A 421 PHE cc_start: 0.7894 (t80) cc_final: 0.7575 (t80) REVERT: A 429 GLU cc_start: 0.8057 (mp0) cc_final: 0.7848 (pm20) REVERT: A 452 MET cc_start: 0.9009 (tpt) cc_final: 0.8643 (tpt) REVERT: A 596 THR cc_start: 0.7229 (OUTLIER) cc_final: 0.6919 (m) outliers start: 9 outliers final: 3 residues processed: 82 average time/residue: 0.0540 time to fit residues: 5.7985 Evaluate side-chains 74 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.111 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 14 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 0.0470 chunk 4 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 212 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.152861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.118791 restraints weight = 5574.660| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.92 r_work: 0.3012 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2385 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= 0.133 Angle : 0.546 10.183 6197 Z= 0.271 Chirality : 0.040 0.142 679 Planarity : 0.004 0.051 753 Dihedral : 4.956 34.921 625 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.93 % Allowed : 12.23 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.36), residues: 548 helix: 1.64 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -1.28 (0.45), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 177 TYR 0.017 0.001 TYR A 69 PHE 0.015 0.001 PHE A 434 TRP 0.010 0.001 TRP A 470 HIS 0.006 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 4552) covalent geometry : angle 0.54629 / 0.27 ( 6195) SS BOND : bond 0.00238 / 0.16 ( 1) SS BOND : angle 0.95023 / 0.61 ( 2) hydrogen bonds : bond 0.03483 / 2.23 ( 277) hydrogen bonds : angle 4.48838 / 3.14 ( 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 83 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.094 Fit side-chains REVERT: A 69 TYR cc_start: 0.9347 (OUTLIER) cc_final: 0.8423 (p90) REVERT: A 125 TYR cc_start: 0.9098 (m-80) cc_final: 0.8716 (m-80) REVERT: A 206 LEU cc_start: 0.8810 (tp) cc_final: 0.8510 (tp) REVERT: A 219 ASP cc_start: 0.8495 (p0) cc_final: 0.8161 (p0) REVERT: A 289 GLN cc_start: 0.8364 (tp40) cc_final: 0.7406 (tt0) REVERT: A 293 ASP cc_start: 0.8593 (m-30) cc_final: 0.8334 (m-30) REVERT: A 421 PHE cc_start: 0.7983 (t80) cc_final: 0.7640 (t80) REVERT: A 452 MET cc_start: 0.9105 (tpt) cc_final: 0.8732 (tpt) REVERT: A 596 THR cc_start: 0.7241 (OUTLIER) cc_final: 0.6896 (m) outliers start: 9 outliers final: 6 residues processed: 81 average time/residue: 0.0362 time to fit residues: 4.0296 Evaluate side-chains 81 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.099 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 54 optimal weight: 0.1980 chunk 20 optimal weight: 0.0050 chunk 33 optimal weight: 0.8980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 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 = 0.3655 r_free = 0.3655 target = 0.150644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.116294 restraints weight = 5601.073| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.93 r_work: 0.3029 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2478 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= 0.131 Angle : 0.562 11.089 6197 Z= 0.279 Chirality : 0.040 0.142 679 Planarity : 0.004 0.050 753 Dihedral : 4.951 32.963 625 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.93 % Allowed : 13.09 % 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 are not related in a simple way. whole: 1.19 (0.36), residues: 548 helix: 1.65 (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 0.001 0.000 ARG A 583 TYR 0.016 0.001 TYR A 69 PHE 0.022 0.002 PHE A 350 TRP 0.010 0.001 TRP A 470 HIS 0.013 0.002 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 4552) covalent geometry : angle 0.56174 / 0.28 ( 6195) SS BOND : bond 0.00151 / 0.10 ( 1) SS BOND : angle 1.48283 / 0.99 ( 2) hydrogen bonds : bond 0.03494 / 2.24 ( 277) hydrogen bonds : angle 4.49566 / 3.13 ( 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: 9 poor density : 73 time to evaluate : 0.164 Fit side-chains REVERT: A 69 TYR cc_start: 0.9327 (OUTLIER) cc_final: 0.8409 (p90) REVERT: A 206 LEU cc_start: 0.8828 (tp) cc_final: 0.8511 (tp) REVERT: A 219 ASP cc_start: 0.8534 (p0) cc_final: 0.8179 (p0) REVERT: A 289 GLN cc_start: 0.8361 (tp40) cc_final: 0.7368 (tt0) REVERT: A 293 ASP cc_start: 0.8565 (m-30) cc_final: 0.8302 (m-30) REVERT: A 421 PHE cc_start: 0.7965 (t80) cc_final: 0.7618 (t80) REVERT: A 452 MET cc_start: 0.9094 (tpt) cc_final: 0.8755 (tpt) REVERT: A 596 THR cc_start: 0.7286 (OUTLIER) cc_final: 0.7021 (m) outliers start: 9 outliers final: 7 residues processed: 80 average time/residue: 0.0515 time to fit residues: 5.6392 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 : 0.098 ------------------------------------------------------------------------------- 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 22 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 ASN A 212 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.151198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.116659 restraints weight = 5627.042| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.94 r_work: 0.2982 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2439 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= 0.159 Angle : 0.582 10.113 6197 Z= 0.289 Chirality : 0.041 0.142 679 Planarity : 0.004 0.050 753 Dihedral : 5.074 33.349 625 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.15 % Allowed : 13.73 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.36), residues: 548 helix: 1.61 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -1.43 (0.44), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 583 TYR 0.018 0.001 TYR A 69 PHE 0.024 0.002 PHE A 191 TRP 0.010 0.001 TRP A 44 HIS 0.013 0.002 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 ( 4552) covalent geometry : angle 0.58146 / 0.29 ( 6195) SS BOND : bond 0.00183 / 0.12 ( 1) SS BOND : angle 1.37715 / 0.87 ( 2) hydrogen bonds : bond 0.03600 / 2.31 ( 277) hydrogen bonds : angle 4.55533 / 3.17 ( 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 80 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.095 Fit side-chains REVERT: A 69 TYR cc_start: 0.9350 (OUTLIER) cc_final: 0.8449 (p90) REVERT: A 125 TYR cc_start: 0.9095 (m-80) cc_final: 0.8710 (m-80) REVERT: A 191 PHE cc_start: 0.7235 (m-80) cc_final: 0.6595 (t80) REVERT: A 219 ASP cc_start: 0.8533 (p0) cc_final: 0.8170 (p0) REVERT: A 289 GLN cc_start: 0.8379 (tp40) cc_final: 0.7392 (tt0) REVERT: A 293 ASP cc_start: 0.8587 (m-30) cc_final: 0.8342 (m-30) REVERT: A 421 PHE cc_start: 0.7974 (t80) cc_final: 0.7625 (t80) REVERT: A 452 MET cc_start: 0.9131 (tpt) cc_final: 0.8762 (tpt) REVERT: A 596 THR cc_start: 0.7317 (OUTLIER) cc_final: 0.7055 (m) outliers start: 10 outliers final: 7 residues processed: 77 average time/residue: 0.0489 time to fit residues: 5.0702 Evaluate side-chains 78 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.157 ------------------------------------------------------------------------------- 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 3 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 chunk 37 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 26 optimal weight: 0.2980 chunk 45 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 212 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.152909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.119182 restraints weight = 5638.357| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.92 r_work: 0.3028 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2577 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= 0.126 Angle : 0.556 10.289 6197 Z= 0.276 Chirality : 0.039 0.142 679 Planarity : 0.004 0.050 753 Dihedral : 4.876 30.433 625 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.50 % Allowed : 15.02 % 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 are not related in a simple way. whole: 1.15 (0.36), residues: 548 helix: 1.67 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -1.48 (0.44), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 583 TYR 0.015 0.001 TYR A 69 PHE 0.022 0.002 PHE A 350 TRP 0.011 0.001 TRP A 470 HIS 0.011 0.002 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 4552) covalent geometry : angle 0.55546 / 0.28 ( 6195) SS BOND : bond 0.00354 / 0.24 ( 1) SS BOND : angle 1.13713 / 0.66 ( 2) hydrogen bonds : bond 0.03428 / 2.20 ( 277) hydrogen bonds : angle 4.47526 / 3.12 ( 816) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1109.30 seconds wall clock time: 19 minutes 37.40 seconds (1177.40 seconds total)