Starting phenix.real_space_refine on Thu Jul 2 00:23:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wmn_66098/07_2026/9wmn_66098_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wmn_66098/07_2026/9wmn_66098.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wmn_66098/07_2026/9wmn_66098_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wmn_66098/07_2026/9wmn_66098_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wmn_66098/07_2026/9wmn_66098.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wmn_66098/07_2026/9wmn_66098.map" } resolution = 2.91 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= -0.003 sd= 0.106 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 34 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 3035 2.51 5 N 657 2.21 5 O 733 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4461 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4263 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 26, 'TRANS': 513} Chain breaks: 1 Chain: "A" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 196 Ad-hoc single atom residues: {' NA': 1, ' CL': 1} Unusual residues: {'CLR': 2, 'Y01': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain breaks: 2 Time building chain proxies: 1.19, per 1000 atoms: 0.27 Number of scatterers: 4461 At special positions: 0 Unit cell: (82.159, 74.69, 73.623, 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 34 16.00 Na 1 11.00 O 733 8.00 N 657 7.00 C 3035 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 166 " distance=2.03 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: 0.45 Conformation dependent library (CDL) restraints added in 181.6 milliseconds 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 982 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 1 sheets defined 78.9% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 40 through 52 removed outlier: 3.538A pdb=" N LEU A 44 " --> pdb=" O TRP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 61 through 69 Processing helix chain 'A' and resid 72 through 86 Proline residue: A 78 - end of helix Processing helix chain 'A' and resid 86 through 102 removed outlier: 3.548A pdb=" N LEU A 90 " --> pdb=" O CYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.601A pdb=" N TRP A 109 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 115 through 147 removed outlier: 3.994A pdb=" N GLY A 119 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET A 135 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 156 removed outlier: 4.189A pdb=" N HIS A 156 " --> pdb=" O PRO A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 214 through 234 Processing helix chain 'A' and resid 247 through 264 removed outlier: 3.517A pdb=" N THR A 263 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 276 removed outlier: 4.042A pdb=" N GLY A 270 " --> pdb=" O GLY A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 284 through 300 removed outlier: 4.243A pdb=" N TRP A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 312 removed outlier: 3.824A pdb=" N TYR A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 353 Processing helix chain 'A' and resid 365 through 376 Proline residue: A 372 - end of helix Processing helix chain 'A' and resid 380 through 415 removed outlier: 3.563A pdb=" N TRP A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 422 through 439 Processing helix chain 'A' and resid 440 through 443 removed outlier: 3.792A pdb=" N THR A 443 " --> pdb=" O ILE A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 440 through 443' Processing helix chain 'A' and resid 445 through 457 removed outlier: 3.644A pdb=" N TRP A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 475 Processing helix chain 'A' and resid 478 through 491 Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 504 through 520 Processing helix chain 'A' and resid 532 through 561 removed outlier: 3.840A pdb=" N SER A 546 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) Proline residue: A 551 - end of helix Processing helix chain 'A' and resid 564 through 574 Processing sheet with id=AA1, first strand: chain 'A' and resid 525 through 526 290 hydrogen bonds defined for protein. 846 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: 0.63 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 637 1.31 - 1.44: 1320 1.44 - 1.56: 2599 1.56 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 4610 Sorted by residual: bond pdb=" C SER A 381 " pdb=" O SER A 381 " ideal model delta sigma weight residual 1.238 1.185 0.053 1.28e-02 6.10e+03 1.68e+01 bond pdb=" N SER A 381 " pdb=" CA SER A 381 " ideal model delta sigma weight residual 1.457 1.505 -0.048 1.41e-02 5.03e+03 1.15e+01 bond pdb=" N ILE A 325 " pdb=" CA ILE A 325 " ideal model delta sigma weight residual 1.461 1.501 -0.040 1.19e-02 7.06e+03 1.14e+01 bond pdb=" CA TYR A 497 " pdb=" C TYR A 497 " ideal model delta sigma weight residual 1.524 1.485 0.039 1.26e-02 6.30e+03 9.59e+00 bond pdb=" N VAL A 592 " pdb=" CA VAL A 592 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.25e-02 6.40e+03 9.54e+00 ... (remaining 4605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 5902 1.65 - 3.31: 336 3.31 - 4.96: 66 4.96 - 6.62: 11 6.62 - 8.27: 2 Bond angle restraints: 6317 Sorted by residual: angle pdb=" N ARG A 321 " pdb=" CA ARG A 321 " pdb=" C ARG A 321 " ideal model delta sigma weight residual 111.11 105.41 5.70 1.20e+00 6.94e-01 2.25e+01 angle pdb=" CA LEU A 395 " pdb=" C LEU A 395 " pdb=" O LEU A 395 " ideal model delta sigma weight residual 120.82 116.31 4.51 1.05e+00 9.07e-01 1.84e+01 angle pdb=" CA SER A 298 " pdb=" C SER A 298 " pdb=" O SER A 298 " ideal model delta sigma weight residual 120.82 116.64 4.18 1.05e+00 9.07e-01 1.58e+01 angle pdb=" CA LEU A 503 " pdb=" C LEU A 503 " pdb=" O LEU A 503 " ideal model delta sigma weight residual 120.42 116.27 4.15 1.06e+00 8.90e-01 1.54e+01 angle pdb=" N ALA A 74 " pdb=" CA ALA A 74 " pdb=" C ALA A 74 " ideal model delta sigma weight residual 111.71 107.36 4.35 1.15e+00 7.56e-01 1.43e+01 ... (remaining 6312 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.45: 2660 24.45 - 48.90: 206 48.90 - 73.35: 28 73.35 - 97.80: 11 97.80 - 122.25: 5 Dihedral angle restraints: 2910 sinusoidal: 1360 harmonic: 1550 Sorted by residual: dihedral pdb=" C10 CLR A 708 " pdb=" C1 CLR A 708 " pdb=" C2 CLR A 708 " pdb=" C3 CLR A 708 " ideal model delta sinusoidal sigma weight residual -56.83 65.42 -122.25 1 3.00e+01 1.11e-03 1.64e+01 dihedral pdb=" C10 CLR A 705 " pdb=" C1 CLR A 705 " pdb=" C2 CLR A 705 " pdb=" C3 CLR A 705 " ideal model delta sinusoidal sigma weight residual -56.83 63.16 -119.99 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" CAT Y01 A 704 " pdb=" CAR Y01 A 704 " pdb=" CBC Y01 A 704 " pdb=" CAV Y01 A 704 " ideal model delta sinusoidal sigma weight residual 58.10 -61.68 119.78 1 3.00e+01 1.11e-03 1.60e+01 ... (remaining 2907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 613 0.062 - 0.124: 91 0.124 - 0.186: 15 0.186 - 0.248: 2 0.248 - 0.310: 1 Chirality restraints: 722 Sorted by residual: chirality pdb=" CBE Y01 A 703 " pdb=" CAP Y01 A 703 " pdb=" CBB Y01 A 703 " pdb=" CBI Y01 A 703 " both_signs ideal model delta sigma weight residual False 2.57 2.26 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA ASN A 134 " pdb=" N ASN A 134 " pdb=" C ASN A 134 " pdb=" CB ASN A 134 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA GLN A 400 " pdb=" N GLN A 400 " pdb=" C GLN A 400 " pdb=" CB GLN A 400 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.43e-01 ... (remaining 719 not shown) Planarity restraints: 734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 321 " -0.019 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C ARG A 321 " 0.064 2.00e-02 2.50e+03 pdb=" O ARG A 321 " -0.024 2.00e-02 2.50e+03 pdb=" N ASP A 322 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 522 " -0.043 5.00e-02 4.00e+02 6.54e-02 6.83e+00 pdb=" N PRO A 523 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 523 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 523 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 471 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.61e+00 pdb=" C LEU A 471 " -0.044 2.00e-02 2.50e+03 pdb=" O LEU A 471 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA A 472 " 0.015 2.00e-02 2.50e+03 ... (remaining 731 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.86: 1553 2.86 - 3.37: 4511 3.37 - 3.88: 7961 3.88 - 4.39: 9631 4.39 - 4.90: 15652 Nonbonded interactions: 39308 Sorted by model distance: nonbonded pdb=" O LEU A 144 " pdb=" OG SER A 147 " model vdw 2.345 3.040 nonbonded pdb=" OG SER A 298 " pdb="NA NA A 701 " model vdw 2.354 3.210 nonbonded pdb=" OH TYR A 456 " pdb=" OE1 GLU A 536 " model vdw 2.383 3.040 nonbonded pdb=" OD1 ASN A 59 " pdb="NA NA A 701 " model vdw 2.424 3.210 nonbonded pdb=" O PHE A 339 " pdb=" OG SER A 343 " model vdw 2.432 3.040 ... (remaining 39303 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: 1.100 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: 6.030 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:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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 : 0.005 0.059 4611 Z= 0.335 Angle : 0.856 8.272 6319 Z= 0.531 Chirality : 0.048 0.310 722 Planarity : 0.006 0.065 734 Dihedral : 17.773 122.253 1925 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 19.65 % Favored : 80.35 % 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: 0.34 (0.35), residues: 536 helix: 0.94 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -1.42 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 420 TYR 0.016 0.002 TYR A 132 PHE 0.012 0.001 PHE A 245 TRP 0.027 0.002 TRP A 215 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.33 ( 4610) covalent geometry : angle 0.85562 / 0.53 ( 6317) SS BOND : bond 0.00267 / 0.14 ( 1) SS BOND : angle 0.52488 / 0.31 ( 2) hydrogen bonds : bond 0.12555 / 8.23 ( 290) hydrogen bonds : angle 5.90039 / 4.04 ( 846) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.143 Fit side-chains REVERT: A 41 THR cc_start: 0.8467 (m) cc_final: 0.8137 (p) REVERT: A 234 LYS cc_start: 0.7513 (tppt) cc_final: 0.7138 (tptt) REVERT: A 274 TYR cc_start: 0.8780 (t80) cc_final: 0.8344 (t80) REVERT: A 468 THR cc_start: 0.8895 (m) cc_final: 0.8652 (m) REVERT: A 577 MET cc_start: 0.8121 (mmt) cc_final: 0.7910 (mmm) REVERT: A 586 ASN cc_start: 0.8354 (m-40) cc_final: 0.8045 (m-40) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.4510 time to fit residues: 52.3109 Evaluate side-chains 77 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 0.3980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 GLN A 159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.139000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.121050 restraints weight = 5185.740| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.83 r_work: 0.3376 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4611 Z= 0.135 Angle : 0.628 9.213 6319 Z= 0.292 Chirality : 0.039 0.208 722 Planarity : 0.005 0.049 734 Dihedral : 10.287 60.166 998 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 4.42 % Allowed : 17.88 % Favored : 77.70 % 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: 1.48 (0.35), residues: 536 helix: 1.84 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -1.09 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 420 TYR 0.013 0.001 TYR A 132 PHE 0.013 0.001 PHE A 245 TRP 0.014 0.001 TRP A 215 HIS 0.002 0.001 HIS A 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 4610) covalent geometry : angle 0.62835 / 0.29 ( 6317) SS BOND : bond 0.00236 / 0.12 ( 1) SS BOND : angle 0.46822 / 0.28 ( 2) hydrogen bonds : bond 0.04581 / 2.96 ( 290) hydrogen bonds : angle 4.69145 / 3.24 ( 846) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.192 Fit side-chains REVERT: A 41 THR cc_start: 0.8315 (m) cc_final: 0.7929 (p) REVERT: A 47 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7456 (mm) REVERT: A 82 MET cc_start: 0.8828 (mmm) cc_final: 0.8611 (mmm) REVERT: A 150 SER cc_start: 0.8522 (t) cc_final: 0.8298 (p) REVERT: A 332 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8108 (mt) REVERT: A 350 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7402 (tp40) REVERT: A 413 ASP cc_start: 0.7872 (m-30) cc_final: 0.7566 (m-30) REVERT: A 418 TYR cc_start: 0.8180 (t80) cc_final: 0.7965 (t80) REVERT: A 460 PHE cc_start: 0.7740 (t80) cc_final: 0.6983 (m-80) REVERT: A 468 THR cc_start: 0.8898 (m) cc_final: 0.8629 (m) REVERT: A 544 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7681 (mp) REVERT: A 577 MET cc_start: 0.8566 (mmt) cc_final: 0.8265 (mmm) outliers start: 20 outliers final: 2 residues processed: 96 average time/residue: 0.3162 time to fit residues: 32.2388 Evaluate side-chains 80 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 546 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 31 optimal weight: 0.1980 chunk 43 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.136894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.118917 restraints weight = 5239.249| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.84 r_work: 0.3337 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4611 Z= 0.142 Angle : 0.568 7.738 6319 Z= 0.269 Chirality : 0.039 0.244 722 Planarity : 0.004 0.038 734 Dihedral : 9.183 59.266 998 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.97 % Allowed : 18.54 % Favored : 77.48 % 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: 1.80 (0.36), residues: 536 helix: 2.03 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.84 (0.47), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 560 TYR 0.016 0.001 TYR A 132 PHE 0.010 0.001 PHE A 389 TRP 0.010 0.001 TRP A 225 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 4610) covalent geometry : angle 0.56770 / 0.27 ( 6317) SS BOND : bond 0.00062 / 0.03 ( 1) SS BOND : angle 0.23035 / 0.13 ( 2) hydrogen bonds : bond 0.04524 / 2.93 ( 290) hydrogen bonds : angle 4.59841 / 3.18 ( 846) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.160 Fit side-chains REVERT: A 41 THR cc_start: 0.8343 (m) cc_final: 0.7968 (p) REVERT: A 46 PHE cc_start: 0.8094 (t80) cc_final: 0.7777 (t80) REVERT: A 47 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7472 (mp) REVERT: A 82 MET cc_start: 0.8972 (mmm) cc_final: 0.8652 (mmp) REVERT: A 150 SER cc_start: 0.8524 (t) cc_final: 0.8270 (p) REVERT: A 168 GLU cc_start: 0.6590 (OUTLIER) cc_final: 0.6134 (tm-30) REVERT: A 295 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8803 (mp) REVERT: A 350 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7379 (tp40) REVERT: A 413 ASP cc_start: 0.7940 (m-30) cc_final: 0.7657 (m-30) REVERT: A 460 PHE cc_start: 0.7686 (t80) cc_final: 0.6923 (m-80) REVERT: A 468 THR cc_start: 0.8919 (m) cc_final: 0.8696 (m) REVERT: A 562 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7557 (pt0) REVERT: A 577 MET cc_start: 0.8564 (mmt) cc_final: 0.8262 (mmm) outliers start: 18 outliers final: 5 residues processed: 89 average time/residue: 0.3926 time to fit residues: 36.7963 Evaluate side-chains 83 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 562 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 0.0010 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.136716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.118434 restraints weight = 5145.348| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.87 r_work: 0.3331 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4611 Z= 0.139 Angle : 0.544 6.416 6319 Z= 0.260 Chirality : 0.038 0.229 722 Planarity : 0.004 0.037 734 Dihedral : 9.100 58.213 998 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.75 % Allowed : 17.22 % Favored : 79.03 % 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: 1.82 (0.36), residues: 536 helix: 2.06 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.86 (0.47), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 420 TYR 0.017 0.001 TYR A 418 PHE 0.019 0.001 PHE A 401 TRP 0.008 0.001 TRP A 109 HIS 0.002 0.000 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 4610) covalent geometry : angle 0.54365 / 0.26 ( 6317) SS BOND : bond 0.00004 / 0.00 ( 1) SS BOND : angle 0.14374 / 0.08 ( 2) hydrogen bonds : bond 0.04399 / 2.85 ( 290) hydrogen bonds : angle 4.54687 / 3.16 ( 846) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.160 Fit side-chains REVERT: A 41 THR cc_start: 0.8261 (m) cc_final: 0.7919 (p) REVERT: A 46 PHE cc_start: 0.7956 (t80) cc_final: 0.7656 (t80) REVERT: A 47 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7358 (mp) REVERT: A 82 MET cc_start: 0.8890 (mmm) cc_final: 0.8600 (mmt) REVERT: A 134 ASN cc_start: 0.8937 (OUTLIER) cc_final: 0.8454 (t0) REVERT: A 150 SER cc_start: 0.8480 (t) cc_final: 0.8181 (p) REVERT: A 168 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.5989 (tm-30) REVERT: A 295 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8749 (mp) REVERT: A 332 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8032 (mt) REVERT: A 350 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7276 (tp40) REVERT: A 413 ASP cc_start: 0.7884 (m-30) cc_final: 0.7592 (m-30) REVERT: A 460 PHE cc_start: 0.7690 (t80) cc_final: 0.6913 (m-80) REVERT: A 562 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7466 (pt0) REVERT: A 577 MET cc_start: 0.8542 (mmt) cc_final: 0.8253 (mmm) outliers start: 17 outliers final: 5 residues processed: 86 average time/residue: 0.3550 time to fit residues: 32.1922 Evaluate side-chains 83 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 562 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 7 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 3 optimal weight: 0.2980 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.131702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.114390 restraints weight = 5313.333| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.62 r_work: 0.3060 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4611 Z= 0.129 Angle : 0.520 6.841 6319 Z= 0.250 Chirality : 0.037 0.211 722 Planarity : 0.004 0.036 734 Dihedral : 9.094 58.147 998 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.53 % Allowed : 18.10 % Favored : 78.37 % 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: 1.90 (0.36), residues: 536 helix: 2.13 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.86 (0.47), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 420 TYR 0.015 0.001 TYR A 132 PHE 0.009 0.001 PHE A 389 TRP 0.008 0.001 TRP A 225 HIS 0.001 0.000 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 4610) covalent geometry : angle 0.52026 / 0.25 ( 6317) SS BOND : bond 0.00030 / 0.02 ( 1) SS BOND : angle 0.10924 / 0.06 ( 2) hydrogen bonds : bond 0.04231 / 2.74 ( 290) hydrogen bonds : angle 4.47796 / 3.12 ( 846) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.098 Fit side-chains REVERT: A 41 THR cc_start: 0.8433 (m) cc_final: 0.8140 (p) REVERT: A 46 PHE cc_start: 0.8127 (t80) cc_final: 0.7827 (t80) REVERT: A 47 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7559 (mp) REVERT: A 82 MET cc_start: 0.8851 (mmm) cc_final: 0.8549 (mmt) REVERT: A 134 ASN cc_start: 0.8874 (OUTLIER) cc_final: 0.8468 (t0) REVERT: A 150 SER cc_start: 0.8532 (t) cc_final: 0.8245 (p) REVERT: A 168 GLU cc_start: 0.6392 (OUTLIER) cc_final: 0.5784 (tm-30) REVERT: A 197 TYR cc_start: 0.8955 (t80) cc_final: 0.8694 (t80) REVERT: A 332 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8062 (mt) REVERT: A 350 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7890 (tm-30) REVERT: A 380 LEU cc_start: 0.8431 (mt) cc_final: 0.8204 (mp) REVERT: A 413 ASP cc_start: 0.7992 (m-30) cc_final: 0.7709 (m-30) REVERT: A 460 PHE cc_start: 0.7737 (t80) cc_final: 0.6995 (m-80) REVERT: A 468 THR cc_start: 0.8888 (m) cc_final: 0.8594 (m) REVERT: A 562 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7438 (pt0) REVERT: A 577 MET cc_start: 0.8547 (mmt) cc_final: 0.8263 (mmm) outliers start: 16 outliers final: 6 residues processed: 85 average time/residue: 0.3893 time to fit residues: 34.8237 Evaluate side-chains 83 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 562 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.130901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.113552 restraints weight = 5400.649| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.65 r_work: 0.3083 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4611 Z= 0.141 Angle : 0.529 7.594 6319 Z= 0.254 Chirality : 0.038 0.215 722 Planarity : 0.004 0.036 734 Dihedral : 9.119 58.397 998 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.09 % Allowed : 18.54 % Favored : 78.37 % 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: 1.87 (0.36), residues: 536 helix: 2.08 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.83 (0.47), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 420 TYR 0.016 0.001 TYR A 132 PHE 0.010 0.001 PHE A 389 TRP 0.008 0.001 TRP A 109 HIS 0.002 0.000 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 4610) covalent geometry : angle 0.52874 / 0.25 ( 6317) SS BOND : bond 0.00064 / 0.03 ( 1) SS BOND : angle 0.17108 / 0.10 ( 2) hydrogen bonds : bond 0.04332 / 2.80 ( 290) hydrogen bonds : angle 4.52193 / 3.15 ( 846) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.159 Fit side-chains REVERT: A 41 THR cc_start: 0.8417 (m) cc_final: 0.8133 (p) REVERT: A 46 PHE cc_start: 0.8161 (t80) cc_final: 0.7841 (t80) REVERT: A 47 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7610 (mp) REVERT: A 82 MET cc_start: 0.8854 (mmm) cc_final: 0.8583 (mmp) REVERT: A 134 ASN cc_start: 0.8868 (OUTLIER) cc_final: 0.8575 (t0) REVERT: A 150 SER cc_start: 0.8538 (t) cc_final: 0.8248 (p) REVERT: A 168 GLU cc_start: 0.6422 (OUTLIER) cc_final: 0.5794 (tm-30) REVERT: A 332 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8064 (mt) REVERT: A 350 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7414 (tp40) REVERT: A 351 GLU cc_start: 0.8055 (tt0) cc_final: 0.7780 (mt-10) REVERT: A 380 LEU cc_start: 0.8454 (mt) cc_final: 0.8237 (mp) REVERT: A 413 ASP cc_start: 0.7985 (m-30) cc_final: 0.7709 (m-30) REVERT: A 460 PHE cc_start: 0.7855 (t80) cc_final: 0.7069 (m-80) REVERT: A 463 MET cc_start: 0.8878 (mtp) cc_final: 0.8554 (mtt) REVERT: A 562 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7451 (pt0) REVERT: A 577 MET cc_start: 0.8539 (mmt) cc_final: 0.8241 (mmm) outliers start: 14 outliers final: 6 residues processed: 77 average time/residue: 0.3949 time to fit residues: 32.1020 Evaluate side-chains 78 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 562 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 HIS A 586 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.128895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.111694 restraints weight = 5355.962| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.64 r_work: 0.3022 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4611 Z= 0.164 Angle : 0.550 7.866 6319 Z= 0.264 Chirality : 0.039 0.226 722 Planarity : 0.004 0.036 734 Dihedral : 9.112 58.534 998 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.31 % Allowed : 18.54 % Favored : 78.15 % 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: 1.81 (0.36), residues: 536 helix: 1.98 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -0.69 (0.49), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 560 TYR 0.016 0.001 TYR A 132 PHE 0.035 0.001 PHE A 401 TRP 0.008 0.001 TRP A 109 HIS 0.002 0.000 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.16 ( 4610) covalent geometry : angle 0.55008 / 0.26 ( 6317) SS BOND : bond 0.00069 / 0.04 ( 1) SS BOND : angle 0.30072 / 0.17 ( 2) hydrogen bonds : bond 0.04560 / 2.95 ( 290) hydrogen bonds : angle 4.61658 / 3.22 ( 846) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.159 Fit side-chains REVERT: A 47 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7619 (mp) REVERT: A 82 MET cc_start: 0.8857 (mmm) cc_final: 0.8506 (mmt) REVERT: A 134 ASN cc_start: 0.8898 (OUTLIER) cc_final: 0.8463 (t0) REVERT: A 150 SER cc_start: 0.8554 (t) cc_final: 0.8257 (p) REVERT: A 168 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.5883 (tm-30) REVERT: A 332 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8068 (mt) REVERT: A 413 ASP cc_start: 0.8020 (m-30) cc_final: 0.7758 (m-30) REVERT: A 418 TYR cc_start: 0.8196 (t80) cc_final: 0.7989 (t80) REVERT: A 460 PHE cc_start: 0.7836 (t80) cc_final: 0.7086 (m-80) REVERT: A 463 MET cc_start: 0.8907 (mtp) cc_final: 0.8581 (mtt) REVERT: A 562 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7560 (pt0) REVERT: A 577 MET cc_start: 0.8552 (mmt) cc_final: 0.8258 (mmm) outliers start: 15 outliers final: 6 residues processed: 75 average time/residue: 0.4160 time to fit residues: 32.8934 Evaluate side-chains 73 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 562 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 42 optimal weight: 0.0870 chunk 24 optimal weight: 0.2980 chunk 19 optimal weight: 0.7980 chunk 49 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 ASN A 156 HIS A 159 ASN A 586 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.132280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.114974 restraints weight = 5343.709| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.64 r_work: 0.3137 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4611 Z= 0.114 Angle : 0.505 8.052 6319 Z= 0.244 Chirality : 0.037 0.193 722 Planarity : 0.003 0.036 734 Dihedral : 8.861 57.901 998 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.43 % Allowed : 20.09 % Favored : 77.48 % 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: 2.03 (0.36), residues: 536 helix: 2.13 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -0.56 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 62 TYR 0.014 0.001 TYR A 132 PHE 0.008 0.001 PHE A 245 TRP 0.010 0.001 TRP A 160 HIS 0.001 0.000 HIS A 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 4610) covalent geometry : angle 0.50463 / 0.24 ( 6317) SS BOND : bond 0.00039 / 0.02 ( 1) SS BOND : angle 0.06252 / 0.03 ( 2) hydrogen bonds : bond 0.04147 / 2.68 ( 290) hydrogen bonds : angle 4.43574 / 3.10 ( 846) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.163 Fit side-chains REVERT: A 46 PHE cc_start: 0.8186 (t80) cc_final: 0.7907 (t80) REVERT: A 47 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7712 (mp) REVERT: A 82 MET cc_start: 0.8844 (mmm) cc_final: 0.8595 (mmp) REVERT: A 134 ASN cc_start: 0.8723 (OUTLIER) cc_final: 0.8381 (t0) REVERT: A 150 SER cc_start: 0.8508 (t) cc_final: 0.8237 (p) REVERT: A 332 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8127 (mt) REVERT: A 413 ASP cc_start: 0.8048 (m-30) cc_final: 0.7756 (m-30) REVERT: A 418 TYR cc_start: 0.8190 (t80) cc_final: 0.7984 (t80) REVERT: A 460 PHE cc_start: 0.7758 (t80) cc_final: 0.7138 (m-80) REVERT: A 463 MET cc_start: 0.8917 (mtp) cc_final: 0.8622 (mtt) REVERT: A 562 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7582 (pt0) REVERT: A 577 MET cc_start: 0.8439 (mmt) cc_final: 0.8156 (mmm) outliers start: 11 outliers final: 3 residues processed: 76 average time/residue: 0.3774 time to fit residues: 30.3590 Evaluate side-chains 74 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 562 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 23 optimal weight: 0.7980 chunk 45 optimal weight: 0.0040 chunk 8 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 ASN A 156 HIS A 586 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.132100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.114799 restraints weight = 5317.154| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.64 r_work: 0.3168 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4611 Z= 0.124 Angle : 0.523 9.400 6319 Z= 0.249 Chirality : 0.037 0.195 722 Planarity : 0.004 0.036 734 Dihedral : 8.814 58.237 998 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.87 % Allowed : 20.75 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.36), residues: 536 helix: 2.15 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -0.51 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 420 TYR 0.013 0.001 TYR A 132 PHE 0.033 0.001 PHE A 401 TRP 0.007 0.001 TRP A 225 HIS 0.001 0.000 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 4610) covalent geometry : angle 0.52301 / 0.25 ( 6317) SS BOND : bond 0.00035 / 0.02 ( 1) SS BOND : angle 0.21165 / 0.11 ( 2) hydrogen bonds : bond 0.04216 / 2.71 ( 290) hydrogen bonds : angle 4.45810 / 3.11 ( 846) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.119 Fit side-chains REVERT: A 47 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7748 (mp) REVERT: A 82 MET cc_start: 0.8843 (mmm) cc_final: 0.8512 (mmt) REVERT: A 134 ASN cc_start: 0.8829 (OUTLIER) cc_final: 0.8496 (t160) REVERT: A 150 SER cc_start: 0.8505 (t) cc_final: 0.8235 (p) REVERT: A 236 VAL cc_start: 0.4390 (OUTLIER) cc_final: 0.4130 (p) REVERT: A 332 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8164 (mt) REVERT: A 413 ASP cc_start: 0.8016 (m-30) cc_final: 0.7726 (m-30) REVERT: A 460 PHE cc_start: 0.7777 (t80) cc_final: 0.7169 (m-80) REVERT: A 463 MET cc_start: 0.8967 (mtp) cc_final: 0.8670 (mtt) REVERT: A 562 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7607 (pt0) REVERT: A 577 MET cc_start: 0.8414 (mmt) cc_final: 0.8140 (mmm) outliers start: 13 outliers final: 5 residues processed: 74 average time/residue: 0.3483 time to fit residues: 27.3214 Evaluate side-chains 76 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 562 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 3 optimal weight: 0.0270 chunk 27 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 ASN A 156 HIS A 586 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.132084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.114819 restraints weight = 5291.785| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.64 r_work: 0.3094 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4611 Z= 0.127 Angle : 0.525 9.614 6319 Z= 0.253 Chirality : 0.037 0.194 722 Planarity : 0.003 0.037 734 Dihedral : 8.752 58.237 998 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.65 % Allowed : 21.19 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.36), residues: 536 helix: 2.15 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -0.46 (0.51), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 420 TYR 0.013 0.001 TYR A 132 PHE 0.009 0.001 PHE A 389 TRP 0.008 0.001 TRP A 225 HIS 0.001 0.000 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 4610) covalent geometry : angle 0.52555 / 0.25 ( 6317) SS BOND : bond 0.00018 / 0.01 ( 1) SS BOND : angle 0.20055 / 0.11 ( 2) hydrogen bonds : bond 0.04241 / 2.73 ( 290) hydrogen bonds : angle 4.46515 / 3.11 ( 846) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.163 Fit side-chains REVERT: A 47 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7715 (mp) REVERT: A 82 MET cc_start: 0.8838 (mmm) cc_final: 0.8506 (mmt) REVERT: A 134 ASN cc_start: 0.8873 (OUTLIER) cc_final: 0.8552 (t160) REVERT: A 150 SER cc_start: 0.8508 (t) cc_final: 0.8231 (p) REVERT: A 236 VAL cc_start: 0.4483 (OUTLIER) cc_final: 0.4204 (p) REVERT: A 332 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8101 (mt) REVERT: A 413 ASP cc_start: 0.8008 (m-30) cc_final: 0.7723 (m-30) REVERT: A 460 PHE cc_start: 0.7780 (t80) cc_final: 0.7110 (m-80) REVERT: A 463 MET cc_start: 0.8951 (mtp) cc_final: 0.8646 (mtt) REVERT: A 562 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7558 (pt0) REVERT: A 577 MET cc_start: 0.8413 (mmt) cc_final: 0.8150 (mmm) outliers start: 12 outliers final: 5 residues processed: 72 average time/residue: 0.3641 time to fit residues: 27.7389 Evaluate side-chains 74 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 562 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 42 optimal weight: 0.0870 chunk 24 optimal weight: 0.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 ASN A 156 HIS A 159 ASN A 586 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.132045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.114808 restraints weight = 5294.180| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.64 r_work: 0.3131 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4611 Z= 0.128 Angle : 0.523 9.566 6319 Z= 0.252 Chirality : 0.037 0.195 722 Planarity : 0.004 0.036 734 Dihedral : 8.692 58.253 998 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.65 % Allowed : 21.41 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.37), residues: 536 helix: 2.17 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -0.42 (0.51), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 420 TYR 0.014 0.001 TYR A 132 PHE 0.035 0.001 PHE A 401 TRP 0.008 0.001 TRP A 160 HIS 0.001 0.000 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 4610) covalent geometry : angle 0.52339 / 0.25 ( 6317) SS BOND : bond 0.00020 / 0.01 ( 1) SS BOND : angle 0.13717 / 0.07 ( 2) hydrogen bonds : bond 0.04248 / 2.74 ( 290) hydrogen bonds : angle 4.46585 / 3.11 ( 846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1513.10 seconds wall clock time: 26 minutes 37.69 seconds (1597.69 seconds total)