Starting phenix.real_space_refine on Sat Apr 4 22:08:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wmn_66098/04_2026/9wmn_66098_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wmn_66098/04_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_66098/04_2026/9wmn_66098_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wmn_66098/04_2026/9wmn_66098_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wmn_66098/04_2026/9wmn_66098.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wmn_66098/04_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-2.1rc1-6017/lib/python3.9/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, 198 Unusual residues: {' CL': 1, ' NA': 1, 'CLR': 2, 'Y01': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 1.17, per 1000 atoms: 0.26 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: 0.35 Conformation dependent library (CDL) restraints added in 220.7 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: 0.11 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: 0.62 Time building geometry restraints manager: 0.45 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 2.470 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 2.470 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: 1.070 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: 0.010 Process input model: 5.680 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 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 covalent geometry : bond 0.00516 ( 4610) covalent geometry : angle 0.85562 ( 6317) SS BOND : bond 0.00267 ( 1) SS BOND : angle 0.52488 ( 2) hydrogen bonds : bond 0.12555 ( 290) hydrogen bonds : angle 5.90039 ( 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 : 0.156 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: 0.4594 time to fit residues: 53.1631 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 : 0.093 ------------------------------------------------------------------------------- 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: 0.5980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3714 r_free = 0.3714 target = 0.138628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.120772 restraints weight = 5188.083| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.82 r_work: 0.3367 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1743 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= 0.140 Angle : 0.626 9.143 6319 Z= 0.291 Chirality : 0.039 0.222 722 Planarity : 0.005 0.047 734 Dihedral : 10.272 61.264 998 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 4.42 % Allowed : 18.10 % 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: 1.50 (0.35), residues: 536 helix: 1.85 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -1.05 (0.46), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 568 TYR 0.014 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 covalent geometry : bond 0.00306 ( 4610) covalent geometry : angle 0.62595 ( 6317) SS BOND : bond 0.00190 ( 1) SS BOND : angle 0.47562 ( 2) hydrogen bonds : bond 0.04589 ( 290) hydrogen bonds : angle 4.68969 ( 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 : 0.126 Fit side-chains REVERT: A 41 THR cc_start: 0.8330 (m) cc_final: 0.7945 (p) REVERT: A 47 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7469 (mm) REVERT: A 82 MET cc_start: 0.8842 (mmm) cc_final: 0.8633 (mmm) REVERT: A 150 SER cc_start: 0.8514 (t) cc_final: 0.8294 (p) REVERT: A 332 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8123 (mt) REVERT: A 350 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7421 (tp40) REVERT: A 413 ASP cc_start: 0.7873 (m-30) cc_final: 0.7572 (m-30) REVERT: A 418 TYR cc_start: 0.8190 (t80) cc_final: 0.7932 (t80) REVERT: A 460 PHE cc_start: 0.7757 (t80) cc_final: 0.7000 (m-80) REVERT: A 468 THR cc_start: 0.8906 (m) cc_final: 0.8641 (m) REVERT: A 544 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7708 (mp) REVERT: A 577 MET cc_start: 0.8556 (mmt) cc_final: 0.8270 (mmm) outliers start: 20 outliers final: 3 residues processed: 96 average time/residue: 0.3618 time to fit residues: 36.7661 Evaluate side-chains 81 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.149 ------------------------------------------------------------------------------- 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 496 LEU 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: 0.7980 chunk 35 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.135499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.117351 restraints weight = 5250.059| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.85 r_work: 0.3323 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4611 Z= 0.153 Angle : 0.579 7.863 6319 Z= 0.274 Chirality : 0.039 0.245 722 Planarity : 0.004 0.038 734 Dihedral : 9.213 59.470 998 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.75 % Allowed : 18.32 % Favored : 77.92 % 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: 1.75 (0.36), residues: 536 helix: 1.99 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.86 (0.48), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 560 TYR 0.016 0.001 TYR A 132 PHE 0.011 0.001 PHE A 389 TRP 0.010 0.001 TRP A 225 HIS 0.002 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 4610) covalent geometry : angle 0.57924 ( 6317) SS BOND : bond 0.00088 ( 1) SS BOND : angle 0.19865 ( 2) hydrogen bonds : bond 0.04624 ( 290) hydrogen bonds : angle 4.63575 ( 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 95 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.158 Fit side-chains REVERT: A 41 THR cc_start: 0.8352 (m) cc_final: 0.7978 (p) REVERT: A 46 PHE cc_start: 0.8114 (t80) cc_final: 0.7792 (t80) REVERT: A 47 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7448 (mp) REVERT: A 82 MET cc_start: 0.8974 (mmm) cc_final: 0.8645 (mmp) REVERT: A 150 SER cc_start: 0.8530 (t) cc_final: 0.8275 (p) REVERT: A 168 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.6103 (tm-30) REVERT: A 295 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8855 (mp) REVERT: A 350 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7388 (tp40) REVERT: A 413 ASP cc_start: 0.7928 (m-30) cc_final: 0.7611 (m-30) REVERT: A 460 PHE cc_start: 0.7716 (t80) cc_final: 0.6970 (m-80) REVERT: A 468 THR cc_start: 0.8920 (m) cc_final: 0.8697 (m) REVERT: A 562 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7540 (pt0) REVERT: A 577 MET cc_start: 0.8562 (mmt) cc_final: 0.8251 (mmm) outliers start: 17 outliers final: 4 residues processed: 89 average time/residue: 0.4110 time to fit residues: 38.4563 Evaluate side-chains 82 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.165 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 30 optimal weight: 0.0770 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3693 r_free = 0.3693 target = 0.136472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.118351 restraints weight = 5137.500| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.83 r_work: 0.3333 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2335 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= 0.131 Angle : 0.535 6.446 6319 Z= 0.256 Chirality : 0.038 0.228 722 Planarity : 0.004 0.038 734 Dihedral : 9.103 58.097 998 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.97 % Allowed : 16.56 % Favored : 79.47 % 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: 1.85 (0.36), residues: 536 helix: 2.07 (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 0.017 0.001 TYR A 418 PHE 0.021 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 covalent geometry : bond 0.00302 ( 4610) covalent geometry : angle 0.53524 ( 6317) SS BOND : bond 0.00029 ( 1) SS BOND : angle 0.11695 ( 2) hydrogen bonds : bond 0.04331 ( 290) hydrogen bonds : angle 4.53272 ( 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: 18 poor density : 74 time to evaluate : 0.130 Fit side-chains REVERT: A 46 PHE cc_start: 0.8117 (t80) cc_final: 0.7827 (t80) REVERT: A 47 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7446 (mp) REVERT: A 82 MET cc_start: 0.8935 (mmm) cc_final: 0.8649 (mmt) REVERT: A 134 ASN cc_start: 0.8895 (OUTLIER) cc_final: 0.8582 (t0) REVERT: A 150 SER cc_start: 0.8477 (t) cc_final: 0.8197 (p) REVERT: A 168 GLU cc_start: 0.6617 (OUTLIER) cc_final: 0.6022 (tm-30) REVERT: A 332 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8159 (mt) REVERT: A 350 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7347 (tp40) REVERT: A 413 ASP cc_start: 0.7940 (m-30) cc_final: 0.7615 (m-30) REVERT: A 460 PHE cc_start: 0.7681 (t80) cc_final: 0.7033 (m-80) REVERT: A 562 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7521 (pt0) REVERT: A 577 MET cc_start: 0.8531 (mmt) cc_final: 0.8228 (mmm) outliers start: 18 outliers final: 5 residues processed: 84 average time/residue: 0.4060 time to fit residues: 35.9350 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 : 0.176 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 40 optimal weight: 0.0980 chunk 37 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3509 r_free = 0.3509 target = 0.131342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.114068 restraints weight = 5336.449| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.62 r_work: 0.3056 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2412 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= 0.131 Angle : 0.525 7.150 6319 Z= 0.252 Chirality : 0.037 0.217 722 Planarity : 0.004 0.036 734 Dihedral : 9.086 58.299 998 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.52 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: 1.87 (0.36), residues: 536 helix: 2.08 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.82 (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 0.009 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 covalent geometry : bond 0.00307 ( 4610) covalent geometry : angle 0.52535 ( 6317) SS BOND : bond 0.00049 ( 1) SS BOND : angle 0.08082 ( 2) hydrogen bonds : bond 0.04275 ( 290) hydrogen bonds : angle 4.50359 ( 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 89 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.103 Fit side-chains REVERT: A 46 PHE cc_start: 0.8111 (t80) cc_final: 0.7809 (t80) REVERT: A 47 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7545 (mp) REVERT: A 82 MET cc_start: 0.8846 (mmm) cc_final: 0.8571 (mmt) REVERT: A 134 ASN cc_start: 0.8890 (OUTLIER) cc_final: 0.8375 (t0) REVERT: A 150 SER cc_start: 0.8545 (t) cc_final: 0.8260 (p) REVERT: A 168 GLU cc_start: 0.6402 (OUTLIER) cc_final: 0.5788 (tm-30) REVERT: A 197 TYR cc_start: 0.8963 (t80) cc_final: 0.8708 (t80) REVERT: A 332 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8065 (mt) REVERT: A 350 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7353 (tp40) REVERT: A 380 LEU cc_start: 0.8428 (mt) cc_final: 0.8219 (mp) REVERT: A 413 ASP cc_start: 0.7954 (m-30) cc_final: 0.7650 (m-30) REVERT: A 460 PHE cc_start: 0.7760 (t80) cc_final: 0.6972 (m-80) REVERT: A 468 THR cc_start: 0.8885 (m) cc_final: 0.8592 (m) REVERT: A 562 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7440 (pt0) REVERT: A 577 MET cc_start: 0.8554 (mmt) cc_final: 0.8268 (mmm) outliers start: 15 outliers final: 5 residues processed: 83 average time/residue: 0.4155 time to fit residues: 36.2208 Evaluate side-chains 83 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.164 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 40 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 52 optimal weight: 0.1980 chunk 26 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3516 r_free = 0.3516 target = 0.131819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.114547 restraints weight = 5389.889| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.63 r_work: 0.3134 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2541 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= 0.124 Angle : 0.515 7.402 6319 Z= 0.247 Chirality : 0.037 0.208 722 Planarity : 0.004 0.035 734 Dihedral : 9.054 58.026 998 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % 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: 1.95 (0.36), residues: 536 helix: 2.13 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.76 (0.48), 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 160 HIS 0.001 0.000 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 4610) covalent geometry : angle 0.51527 ( 6317) SS BOND : bond 0.00065 ( 1) SS BOND : angle 0.09499 ( 2) hydrogen bonds : bond 0.04185 ( 290) hydrogen bonds : angle 4.45866 ( 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 86 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.161 Fit side-chains REVERT: A 46 PHE cc_start: 0.8280 (t80) cc_final: 0.7988 (t80) REVERT: A 47 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7698 (mp) REVERT: A 82 MET cc_start: 0.8861 (mmm) cc_final: 0.8592 (mmp) REVERT: A 150 SER cc_start: 0.8509 (t) cc_final: 0.8248 (p) REVERT: A 168 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.5808 (tm-30) REVERT: A 197 TYR cc_start: 0.8953 (t80) cc_final: 0.8707 (t80) REVERT: A 332 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8180 (mt) REVERT: A 350 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7459 (tp40) REVERT: A 351 GLU cc_start: 0.8045 (tt0) cc_final: 0.7807 (mt-10) REVERT: A 413 ASP cc_start: 0.8029 (m-30) cc_final: 0.7750 (m-30) REVERT: A 460 PHE cc_start: 0.7737 (t80) cc_final: 0.7105 (m-80) REVERT: A 562 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7615 (pt0) REVERT: A 577 MET cc_start: 0.8511 (mmt) cc_final: 0.8241 (mmm) outliers start: 14 outliers final: 6 residues processed: 80 average time/residue: 0.4175 time to fit residues: 35.1965 Evaluate side-chains 82 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.160 ------------------------------------------------------------------------------- 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 332 ILE Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 544 LEU 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: 0.9990 chunk 40 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 3 optimal weight: 0.1980 chunk 51 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3503 r_free = 0.3503 target = 0.130751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.113587 restraints weight = 5354.718| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.63 r_work: 0.3020 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2571 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= 0.138 Angle : 0.528 7.558 6319 Z= 0.252 Chirality : 0.038 0.212 722 Planarity : 0.004 0.036 734 Dihedral : 9.057 58.394 998 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.65 % Allowed : 18.98 % 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: 1.95 (0.36), residues: 536 helix: 2.12 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.72 (0.49), residues: 161 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 0.032 0.001 PHE A 401 TRP 0.007 0.001 TRP A 109 HIS 0.002 0.000 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 4610) covalent geometry : angle 0.52789 ( 6317) SS BOND : bond 0.00043 ( 1) SS BOND : angle 0.14054 ( 2) hydrogen bonds : bond 0.04278 ( 290) hydrogen bonds : angle 4.51508 ( 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 77 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.166 Fit side-chains REVERT: A 47 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7704 (mp) REVERT: A 82 MET cc_start: 0.8852 (mmm) cc_final: 0.8582 (mmt) REVERT: A 134 ASN cc_start: 0.9037 (t0) cc_final: 0.8791 (t160) REVERT: A 150 SER cc_start: 0.8512 (t) cc_final: 0.8225 (p) REVERT: A 168 GLU cc_start: 0.6446 (OUTLIER) cc_final: 0.5780 (tm-30) REVERT: A 332 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8078 (mt) REVERT: A 413 ASP cc_start: 0.7999 (m-30) cc_final: 0.7722 (m-30) REVERT: A 460 PHE cc_start: 0.7803 (t80) cc_final: 0.7098 (m-80) REVERT: A 562 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7577 (pt0) REVERT: A 577 MET cc_start: 0.8537 (mmt) cc_final: 0.8251 (mmm) outliers start: 12 outliers final: 6 residues processed: 73 average time/residue: 0.3690 time to fit residues: 28.4136 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 : 0.162 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 2 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3505 r_free = 0.3505 target = 0.131058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.113847 restraints weight = 5359.016| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.63 r_work: 0.3087 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2628 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= 0.131 Angle : 0.518 7.974 6319 Z= 0.249 Chirality : 0.037 0.205 722 Planarity : 0.004 0.036 734 Dihedral : 8.939 58.111 998 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.09 % Allowed : 18.98 % Favored : 77.92 % 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: 1.99 (0.36), residues: 536 helix: 2.12 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -0.62 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 420 TYR 0.015 0.001 TYR A 132 PHE 0.009 0.001 PHE A 389 TRP 0.007 0.001 TRP A 109 HIS 0.001 0.000 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 4610) covalent geometry : angle 0.51819 ( 6317) SS BOND : bond 0.00054 ( 1) SS BOND : angle 0.16055 ( 2) hydrogen bonds : bond 0.04232 ( 290) hydrogen bonds : angle 4.48391 ( 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 82 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.096 Fit side-chains REVERT: A 47 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7658 (mp) REVERT: A 82 MET cc_start: 0.8841 (mmm) cc_final: 0.8580 (mmt) REVERT: A 134 ASN cc_start: 0.9055 (t0) cc_final: 0.8847 (t160) REVERT: A 150 SER cc_start: 0.8524 (t) cc_final: 0.8234 (p) REVERT: A 168 GLU cc_start: 0.6646 (OUTLIER) cc_final: 0.5946 (tm-30) REVERT: A 236 VAL cc_start: 0.4271 (OUTLIER) cc_final: 0.4017 (p) REVERT: A 332 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8053 (mt) REVERT: A 413 ASP cc_start: 0.8007 (m-30) cc_final: 0.7735 (m-30) REVERT: A 418 TYR cc_start: 0.8187 (t80) cc_final: 0.7963 (t80) REVERT: A 460 PHE cc_start: 0.7772 (t80) cc_final: 0.7073 (m-80) REVERT: A 562 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7551 (pt0) REVERT: A 577 MET cc_start: 0.8518 (mmt) cc_final: 0.8224 (mmm) outliers start: 14 outliers final: 7 residues processed: 78 average time/residue: 0.3494 time to fit residues: 28.7223 Evaluate side-chains 76 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.147 ------------------------------------------------------------------------------- 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 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 545 LEU Chi-restraints excluded: chain A residue 546 SER 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: 2.9990 chunk 45 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3496 r_free = 0.3496 target = 0.130202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.113086 restraints weight = 5327.057| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.63 r_work: 0.3012 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4611 Z= 0.143 Angle : 0.529 8.316 6319 Z= 0.254 Chirality : 0.038 0.211 722 Planarity : 0.004 0.036 734 Dihedral : 8.869 58.424 998 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.87 % Allowed : 20.31 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.36), residues: 536 helix: 2.09 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -0.56 (0.51), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 66 TYR 0.016 0.001 TYR A 132 PHE 0.030 0.001 PHE A 401 TRP 0.008 0.001 TRP A 225 HIS 0.002 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 4610) covalent geometry : angle 0.52879 ( 6317) SS BOND : bond 0.00070 ( 1) SS BOND : angle 0.22612 ( 2) hydrogen bonds : bond 0.04329 ( 290) hydrogen bonds : angle 4.53485 ( 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 81 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.156 Fit side-chains REVERT: A 47 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7670 (mp) REVERT: A 82 MET cc_start: 0.8835 (mmm) cc_final: 0.8492 (mmt) REVERT: A 134 ASN cc_start: 0.9078 (t0) cc_final: 0.8832 (t160) REVERT: A 150 SER cc_start: 0.8528 (t) cc_final: 0.8235 (p) REVERT: A 168 GLU cc_start: 0.6695 (OUTLIER) cc_final: 0.5955 (tm-30) REVERT: A 236 VAL cc_start: 0.4391 (OUTLIER) cc_final: 0.4110 (p) REVERT: A 332 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8037 (mt) REVERT: A 413 ASP cc_start: 0.8019 (m-30) cc_final: 0.7759 (m-30) REVERT: A 460 PHE cc_start: 0.7805 (t80) cc_final: 0.7067 (m-80) REVERT: A 562 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7551 (pt0) REVERT: A 577 MET cc_start: 0.8532 (mmt) cc_final: 0.8229 (mmm) outliers start: 13 outliers final: 7 residues processed: 76 average time/residue: 0.3686 time to fit residues: 29.5230 Evaluate side-chains 76 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.150 ------------------------------------------------------------------------------- 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 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 545 LEU Chi-restraints excluded: chain A residue 546 SER 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: 0.0370 chunk 27 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.0470 chunk 28 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3524 r_free = 0.3524 target = 0.132737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.115663 restraints weight = 5298.982| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.62 r_work: 0.3144 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2757 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= 0.114 Angle : 0.514 9.161 6319 Z= 0.247 Chirality : 0.037 0.187 722 Planarity : 0.003 0.037 734 Dihedral : 8.675 57.939 998 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.87 % Allowed : 20.53 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.37), residues: 536 helix: 2.22 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -0.48 (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 0.008 0.001 PHE A 389 TRP 0.009 0.001 TRP A 160 HIS 0.001 0.000 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 4610) covalent geometry : angle 0.51359 ( 6317) SS BOND : bond 0.00002 ( 1) SS BOND : angle 0.03908 ( 2) hydrogen bonds : bond 0.04053 ( 290) hydrogen bonds : angle 4.41720 ( 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 79 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.182 Fit side-chains REVERT: A 47 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7777 (mp) REVERT: A 82 MET cc_start: 0.8826 (mmm) cc_final: 0.8505 (mmt) REVERT: A 150 SER cc_start: 0.8482 (t) cc_final: 0.8226 (p) REVERT: A 236 VAL cc_start: 0.4446 (OUTLIER) cc_final: 0.4158 (p) REVERT: A 413 ASP cc_start: 0.8017 (m-30) cc_final: 0.7726 (m-30) REVERT: A 460 PHE cc_start: 0.7753 (t80) cc_final: 0.7143 (m-80) REVERT: A 562 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7606 (pt0) REVERT: A 577 MET cc_start: 0.8395 (mmt) cc_final: 0.8140 (mmm) outliers start: 13 outliers final: 5 residues processed: 73 average time/residue: 0.3716 time to fit residues: 28.6645 Evaluate side-chains 70 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 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 190 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 236 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/iotbx/cli_parser.py", line 995, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.5343 > 50: distance: 77 - 94: 11.248 distance: 81 - 99: 10.049 distance: 86 - 107: 10.131 distance: 89 - 94: 9.432 distance: 90 - 119: 3.691 distance: 94 - 95: 9.630 distance: 95 - 96: 14.451 distance: 95 - 98: 24.775 distance: 96 - 97: 11.334 distance: 96 - 99: 7.923 distance: 97 - 127: 9.737 distance: 99 - 100: 7.311 distance: 100 - 101: 10.226 distance: 100 - 103: 8.678 distance: 101 - 102: 13.572 distance: 101 - 107: 8.582 distance: 102 - 135: 16.239 distance: 103 - 104: 10.969 distance: 104 - 105: 9.927 distance: 105 - 106: 13.898 distance: 107 - 108: 5.415 distance: 108 - 109: 8.935 distance: 108 - 111: 4.401 distance: 109 - 110: 6.851 distance: 109 - 119: 7.272 distance: 110 - 139: 23.665 distance: 111 - 112: 6.753 distance: 112 - 114: 4.325 distance: 113 - 115: 6.041 distance: 114 - 116: 5.883 distance: 115 - 117: 4.365 distance: 117 - 118: 5.111 distance: 119 - 120: 12.906 distance: 120 - 121: 10.124 distance: 120 - 123: 22.254 distance: 121 - 122: 14.670 distance: 121 - 127: 17.129 distance: 123 - 124: 16.618 distance: 124 - 125: 3.046 distance: 124 - 126: 15.775 distance: 127 - 128: 16.375 distance: 128 - 129: 38.499 distance: 128 - 131: 16.632 distance: 129 - 130: 14.866 distance: 129 - 135: 41.549 distance: 131 - 132: 32.562 distance: 132 - 133: 4.752 distance: 133 - 134: 13.788 distance: 135 - 136: 36.462 distance: 136 - 137: 12.263 distance: 137 - 138: 9.411 distance: 137 - 139: 11.210 distance: 139 - 140: 14.629 distance: 140 - 141: 14.891 distance: 140 - 143: 19.522 distance: 141 - 142: 25.493 distance: 141 - 147: 38.870 distance: 143 - 144: 31.155 distance: 144 - 145: 10.172 distance: 144 - 146: 15.129 distance: 147 - 148: 6.468 distance: 148 - 149: 7.877 distance: 148 - 151: 6.409 distance: 149 - 150: 9.138 distance: 149 - 155: 13.857 distance: 151 - 152: 5.961 distance: 151 - 153: 3.999 distance: 152 - 154: 16.280 distance: 155 - 156: 15.558 distance: 156 - 157: 13.354 distance: 156 - 159: 19.042 distance: 157 - 158: 12.412 distance: 157 - 163: 9.092 distance: 159 - 160: 4.394 distance: 160 - 161: 6.965 distance: 160 - 162: 33.293 distance: 163 - 164: 9.338 distance: 164 - 165: 3.989 distance: 164 - 167: 10.628 distance: 165 - 166: 6.944 distance: 165 - 170: 5.297 distance: 167 - 168: 19.167 distance: 167 - 169: 10.239