Starting phenix.real_space_refine on Wed Feb 4 03:57:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pmd_71735/02_2026/9pmd_71735.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pmd_71735/02_2026/9pmd_71735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pmd_71735/02_2026/9pmd_71735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pmd_71735/02_2026/9pmd_71735.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pmd_71735/02_2026/9pmd_71735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pmd_71735/02_2026/9pmd_71735.map" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 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 27 5.16 5 Na 1 4.78 5 C 2761 2.51 5 N 673 2.21 5 O 731 1.98 5 H 4242 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8435 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 8432 Classifications: {'peptide': 528} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 25, 'TRANS': 502} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1, 'water': 2} Link IDs: {None: 2} Time building chain proxies: 1.38, per 1000 atoms: 0.16 Number of scatterers: 8435 At special positions: 0 Unit cell: (112.88, 71.38, 69.72, 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) S 27 16.00 Na 1 11.00 O 731 8.00 N 673 7.00 C 2761 6.00 H 4242 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 113 " distance=2.03 Simple disulfide: pdb=" SG CYS A 81 " - pdb=" SG CYS A 136 " 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: 0.56 Conformation dependent library (CDL) restraints added in 114.7 milliseconds 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 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: 34 helices and 2 sheets defined 78.0% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 Processing helix chain 'A' and resid 9 through 12 Processing helix chain 'A' and resid 15 through 28 Processing helix chain 'A' and resid 29 through 37 removed outlier: 3.677A pdb=" N PHE A 34 " --> pdb=" O ILE A 30 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY A 36 " --> pdb=" O ASN A 32 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU A 37 " --> pdb=" O GLY A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 59 through 64 removed outlier: 3.528A pdb=" N ASN A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 95 removed outlier: 3.612A pdb=" N PHE A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 133 Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 140 through 168 removed outlier: 3.537A pdb=" N LEU A 144 " --> pdb=" O TRP A 140 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 145 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 159 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY A 161 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLN A 162 " --> pdb=" O PHE A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 187 Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 192 through 222 removed outlier: 3.715A pdb=" N ALA A 214 " --> pdb=" O ASN A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 233 removed outlier: 3.647A pdb=" N ILE A 229 " --> pdb=" O SER A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 253 Proline residue: A 247 - end of helix removed outlier: 3.801A pdb=" N PHE A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 270 Proline residue: A 266 - end of helix removed outlier: 3.769A pdb=" N LEU A 269 " --> pdb=" O MET A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 276 removed outlier: 4.082A pdb=" N TRP A 275 " --> pdb=" O ALA A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 289 through 305 Processing helix chain 'A' and resid 316 through 320 Processing helix chain 'A' and resid 330 through 335 Processing helix chain 'A' and resid 337 through 364 Processing helix chain 'A' and resid 365 through 368 Processing helix chain 'A' and resid 371 through 382 Processing helix chain 'A' and resid 382 through 397 Processing helix chain 'A' and resid 398 through 416 removed outlier: 3.557A pdb=" N PHE A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 420 Processing helix chain 'A' and resid 421 through 424 Processing helix chain 'A' and resid 425 through 454 removed outlier: 4.158A pdb=" N THR A 429 " --> pdb=" O TYR A 425 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR A 447 " --> pdb=" O PHE A 443 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 458 through 483 Proline residue: A 478 - end of helix removed outlier: 3.734A pdb=" N VAL A 481 " --> pdb=" O SER A 477 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 483 " --> pdb=" O TYR A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 486 No H-bonds generated for 'chain 'A' and resid 484 through 486' Processing helix chain 'A' and resid 489 through 507 removed outlier: 3.669A pdb=" N LEU A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 72 Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 84 259 hydrogen bonds defined for protein. 726 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: 1.76 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 4239 1.04 - 1.23: 63 1.23 - 1.43: 1767 1.43 - 1.63: 2428 1.63 - 1.82: 47 Bond restraints: 8544 Sorted by residual: bond pdb=" CB LYS A 325 " pdb=" CG LYS A 325 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.74e-01 bond pdb=" CB GLN A 107 " pdb=" CG GLN A 107 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.20e-01 bond pdb=" C VAL A 198 " pdb=" O VAL A 198 " ideal model delta sigma weight residual 1.237 1.246 -0.009 1.17e-02 7.31e+03 6.10e-01 bond pdb=" CB CYS A 113 " pdb=" SG CYS A 113 " ideal model delta sigma weight residual 1.808 1.783 0.025 3.30e-02 9.18e+02 5.90e-01 bond pdb=" CG LYS A 325 " pdb=" CD LYS A 325 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 4.70e-01 ... (remaining 8539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 15009 1.46 - 2.92: 397 2.92 - 4.37: 35 4.37 - 5.83: 4 5.83 - 7.29: 1 Bond angle restraints: 15446 Sorted by residual: angle pdb=" CB LYS A 325 " pdb=" CG LYS A 325 " pdb=" CD LYS A 325 " ideal model delta sigma weight residual 111.30 118.59 -7.29 2.30e+00 1.89e-01 1.00e+01 angle pdb=" CA LYS A 325 " pdb=" CB LYS A 325 " pdb=" CG LYS A 325 " ideal model delta sigma weight residual 114.10 119.07 -4.97 2.00e+00 2.50e-01 6.17e+00 angle pdb=" CA CYS A 50 " pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " ideal model delta sigma weight residual 114.40 119.11 -4.71 2.30e+00 1.89e-01 4.19e+00 angle pdb=" CB GLN A 107 " pdb=" CG GLN A 107 " pdb=" CD GLN A 107 " ideal model delta sigma weight residual 112.60 116.08 -3.48 1.70e+00 3.46e-01 4.19e+00 angle pdb=" N TYR A 396 " pdb=" CA TYR A 396 " pdb=" C TYR A 396 " ideal model delta sigma weight residual 114.39 117.22 -2.83 1.45e+00 4.76e-01 3.80e+00 ... (remaining 15441 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 3610 16.82 - 33.64: 276 33.64 - 50.45: 84 50.45 - 67.27: 54 67.27 - 84.09: 11 Dihedral angle restraints: 4035 sinusoidal: 2144 harmonic: 1891 Sorted by residual: dihedral pdb=" CA CYS A 50 " pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " pdb=" SG CYS A 113 " ideal model delta sinusoidal sigma weight residual -73.00 -4.11 -68.89 1 2.00e+01 2.50e-03 1.54e+01 dihedral pdb=" CG ARG A 49 " pdb=" CD ARG A 49 " pdb=" NE ARG A 49 " pdb=" CZ ARG A 49 " ideal model delta sinusoidal sigma weight residual 180.00 138.03 41.97 2 1.50e+01 4.44e-03 9.54e+00 dihedral pdb=" CB MET A 445 " pdb=" CG MET A 445 " pdb=" SD MET A 445 " pdb=" CE MET A 445 " ideal model delta sinusoidal sigma weight residual -180.00 -120.31 -59.69 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 4032 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 528 0.044 - 0.087: 120 0.087 - 0.131: 23 0.131 - 0.174: 1 0.174 - 0.218: 1 Chirality restraints: 673 Sorted by residual: chirality pdb=" CA TRP A 275 " pdb=" N TRP A 275 " pdb=" C TRP A 275 " pdb=" CB TRP A 275 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB VAL A 197 " pdb=" CA VAL A 197 " pdb=" CG1 VAL A 197 " pdb=" CG2 VAL A 197 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA ILE A 277 " pdb=" N ILE A 277 " pdb=" C ILE A 277 " pdb=" CB ILE A 277 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 ... (remaining 670 not shown) Planarity restraints: 1228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 207 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" C GLN A 207 " 0.036 2.00e-02 2.50e+03 pdb=" O GLN A 207 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE A 208 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 205 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" C MET A 205 " -0.030 2.00e-02 2.50e+03 pdb=" O MET A 205 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY A 206 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 358 " -0.009 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" C TYR A 358 " 0.029 2.00e-02 2.50e+03 pdb=" O TYR A 358 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE A 359 " -0.010 2.00e-02 2.50e+03 ... (remaining 1225 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 404 2.19 - 2.79: 16653 2.79 - 3.39: 23600 3.39 - 4.00: 29937 4.00 - 4.60: 46909 Nonbonded interactions: 117503 Sorted by model distance: nonbonded pdb=" OD1 ASP A 165 " pdb="HH12 ARG A 169 " model vdw 1.584 2.450 nonbonded pdb=" OE1 GLN A 180 " pdb="HD22 ASN A 210 " model vdw 1.636 2.450 nonbonded pdb=" OE1 GLU A 13 " pdb=" HG SER A 225 " model vdw 1.649 2.450 nonbonded pdb=" O ASP A 371 " pdb="HD21 ASN A 375 " model vdw 1.670 2.450 nonbonded pdb=" OD2 ASP A 364 " pdb=" HH TYR A 492 " model vdw 1.684 2.450 ... (remaining 117498 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: 2.600 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: 0.030 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.940 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:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 16.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 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 : 0.002 0.028 4304 Z= 0.113 Angle : 0.570 7.288 5861 Z= 0.316 Chirality : 0.039 0.218 673 Planarity : 0.007 0.054 726 Dihedral : 13.831 81.298 1524 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.87 % Allowed : 14.38 % Favored : 84.75 % 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: 1.70 (0.38), residues: 526 helix: 1.48 (0.30), residues: 318 sheet: None (None), residues: 0 loop : 0.76 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.003 ARG A 254 TYR 0.013 0.004 TYR A 396 PHE 0.008 0.001 PHE A 200 TRP 0.010 0.001 TRP A 256 HIS 0.002 0.001 HIS A 79 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 4302) covalent geometry : angle 0.56639 ( 5857) SS BOND : bond 0.00271 ( 2) SS BOND : angle 2.43489 ( 4) hydrogen bonds : bond 0.15821 ( 259) hydrogen bonds : angle 5.28880 ( 726) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8190 (mm-30) REVERT: A 62 TRP cc_start: 0.8498 (m100) cc_final: 0.8097 (m100) REVERT: A 191 LYS cc_start: 0.8544 (mttt) cc_final: 0.8340 (mttm) REVERT: A 325 LYS cc_start: 0.9170 (tppp) cc_final: 0.8832 (ptpt) REVERT: A 326 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8619 (mm-40) outliers start: 4 outliers final: 1 residues processed: 60 average time/residue: 0.9008 time to fit residues: 56.4787 Evaluate side-chains 50 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.0980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.103955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.084885 restraints weight = 21326.172| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.39 r_work: 0.2879 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4304 Z= 0.129 Angle : 0.517 5.534 5861 Z= 0.272 Chirality : 0.037 0.121 673 Planarity : 0.004 0.036 726 Dihedral : 3.487 15.624 576 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.96 % Allowed : 13.07 % Favored : 84.97 % 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: 1.86 (0.38), residues: 526 helix: 1.65 (0.29), residues: 338 sheet: None (None), residues: 0 loop : 0.63 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 488 TYR 0.008 0.001 TYR A 447 PHE 0.011 0.001 PHE A 34 TRP 0.011 0.001 TRP A 256 HIS 0.002 0.001 HIS A 79 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 4302) covalent geometry : angle 0.51525 ( 5857) SS BOND : bond 0.00125 ( 2) SS BOND : angle 1.72857 ( 4) hydrogen bonds : bond 0.05059 ( 259) hydrogen bonds : angle 4.36719 ( 726) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: A 200 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8545 (t80) REVERT: A 325 LYS cc_start: 0.9148 (tppp) cc_final: 0.8841 (ptmt) REVERT: A 326 GLN cc_start: 0.8797 (mm-40) cc_final: 0.8584 (tp-100) outliers start: 9 outliers final: 4 residues processed: 60 average time/residue: 0.9585 time to fit residues: 60.0063 Evaluate side-chains 54 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 520 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 20 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 51 optimal weight: 0.0980 chunk 38 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.104239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.084777 restraints weight = 21239.983| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.44 r_work: 0.2864 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4304 Z= 0.114 Angle : 0.479 4.798 5861 Z= 0.250 Chirality : 0.037 0.122 673 Planarity : 0.005 0.086 726 Dihedral : 3.508 15.768 576 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.74 % Allowed : 13.29 % Favored : 84.97 % 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: 2.12 (0.38), residues: 526 helix: 1.88 (0.29), residues: 338 sheet: None (None), residues: 0 loop : 0.68 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 488 TYR 0.008 0.001 TYR A 239 PHE 0.011 0.001 PHE A 34 TRP 0.010 0.001 TRP A 256 HIS 0.003 0.001 HIS A 79 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 4302) covalent geometry : angle 0.47724 ( 5857) SS BOND : bond 0.00172 ( 2) SS BOND : angle 1.60213 ( 4) hydrogen bonds : bond 0.04566 ( 259) hydrogen bonds : angle 4.13291 ( 726) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 200 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.8593 (t80) REVERT: A 325 LYS cc_start: 0.9123 (tppp) cc_final: 0.8833 (ptmt) outliers start: 8 outliers final: 1 residues processed: 55 average time/residue: 1.0311 time to fit residues: 59.0500 Evaluate side-chains 51 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 520 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 41 optimal weight: 0.4980 chunk 7 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.104493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.084704 restraints weight = 21483.902| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.45 r_work: 0.2870 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4304 Z= 0.127 Angle : 0.473 4.850 5861 Z= 0.248 Chirality : 0.037 0.122 673 Planarity : 0.004 0.047 726 Dihedral : 3.496 16.605 576 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.53 % Allowed : 13.94 % Favored : 84.53 % 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: 2.21 (0.37), residues: 526 helix: 1.96 (0.29), residues: 338 sheet: None (None), residues: 0 loop : 0.70 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 488 TYR 0.007 0.001 TYR A 447 PHE 0.011 0.001 PHE A 34 TRP 0.010 0.001 TRP A 256 HIS 0.002 0.001 HIS A 79 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 4302) covalent geometry : angle 0.47128 ( 5857) SS BOND : bond 0.00178 ( 2) SS BOND : angle 1.62583 ( 4) hydrogen bonds : bond 0.04502 ( 259) hydrogen bonds : angle 4.05060 ( 726) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 200 PHE cc_start: 0.9027 (OUTLIER) cc_final: 0.8715 (t80) REVERT: A 325 LYS cc_start: 0.9103 (tppp) cc_final: 0.8856 (ptmt) outliers start: 7 outliers final: 3 residues processed: 59 average time/residue: 0.9207 time to fit residues: 56.7986 Evaluate side-chains 54 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 520 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 36 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.104055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.084329 restraints weight = 21237.660| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.38 r_work: 0.2866 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4304 Z= 0.141 Angle : 0.482 4.891 5861 Z= 0.252 Chirality : 0.037 0.139 673 Planarity : 0.003 0.040 726 Dihedral : 3.512 17.154 576 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.96 % Allowed : 14.16 % Favored : 83.88 % 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: 2.17 (0.37), residues: 526 helix: 1.96 (0.29), residues: 338 sheet: None (None), residues: 0 loop : 0.61 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 488 TYR 0.008 0.001 TYR A 239 PHE 0.011 0.001 PHE A 34 TRP 0.010 0.001 TRP A 256 HIS 0.002 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 4302) covalent geometry : angle 0.48017 ( 5857) SS BOND : bond 0.00216 ( 2) SS BOND : angle 1.59707 ( 4) hydrogen bonds : bond 0.04579 ( 259) hydrogen bonds : angle 4.03411 ( 726) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 200 PHE cc_start: 0.9103 (OUTLIER) cc_final: 0.8798 (t80) REVERT: A 325 LYS cc_start: 0.9069 (tppp) cc_final: 0.8838 (ptpt) outliers start: 9 outliers final: 3 residues processed: 57 average time/residue: 0.9666 time to fit residues: 57.4497 Evaluate side-chains 52 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 520 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 0.0670 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.102923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.083190 restraints weight = 21221.382| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.41 r_work: 0.2853 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 4304 Z= 0.150 Angle : 0.481 4.916 5861 Z= 0.253 Chirality : 0.037 0.153 673 Planarity : 0.003 0.033 726 Dihedral : 3.540 17.504 576 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.31 % Allowed : 15.03 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.37), residues: 526 helix: 1.95 (0.28), residues: 338 sheet: None (None), residues: 0 loop : 0.56 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 488 TYR 0.009 0.001 TYR A 447 PHE 0.012 0.001 PHE A 34 TRP 0.009 0.001 TRP A 256 HIS 0.002 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 4302) covalent geometry : angle 0.47974 ( 5857) SS BOND : bond 0.00140 ( 2) SS BOND : angle 1.60365 ( 4) hydrogen bonds : bond 0.04664 ( 259) hydrogen bonds : angle 4.04134 ( 726) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 200 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.8806 (t80) outliers start: 6 outliers final: 2 residues processed: 54 average time/residue: 1.0008 time to fit residues: 56.2822 Evaluate side-chains 51 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 347 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.104411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.084775 restraints weight = 21476.574| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.40 r_work: 0.2866 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4304 Z= 0.121 Angle : 0.492 7.404 5861 Z= 0.254 Chirality : 0.037 0.157 673 Planarity : 0.003 0.029 726 Dihedral : 3.450 17.414 575 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.31 % Allowed : 16.12 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.37), residues: 526 helix: 2.04 (0.28), residues: 338 sheet: None (None), residues: 0 loop : 0.59 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 488 TYR 0.008 0.001 TYR A 239 PHE 0.011 0.001 PHE A 34 TRP 0.009 0.001 TRP A 256 HIS 0.001 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 4302) covalent geometry : angle 0.49032 ( 5857) SS BOND : bond 0.00072 ( 2) SS BOND : angle 1.57619 ( 4) hydrogen bonds : bond 0.04417 ( 259) hydrogen bonds : angle 3.97394 ( 726) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 200 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.8787 (t80) REVERT: A 325 LYS cc_start: 0.9034 (tppp) cc_final: 0.8761 (ptmt) outliers start: 6 outliers final: 3 residues processed: 53 average time/residue: 0.7731 time to fit residues: 42.9431 Evaluate side-chains 51 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 520 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 9 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.104140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.084600 restraints weight = 21222.857| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.38 r_work: 0.2877 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4304 Z= 0.131 Angle : 0.484 6.343 5861 Z= 0.251 Chirality : 0.037 0.170 673 Planarity : 0.003 0.029 726 Dihedral : 3.442 17.397 575 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.53 % Allowed : 15.90 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.37), residues: 526 helix: 2.01 (0.28), residues: 339 sheet: None (None), residues: 0 loop : 0.54 (0.47), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 488 TYR 0.008 0.001 TYR A 447 PHE 0.011 0.001 PHE A 34 TRP 0.010 0.001 TRP A 62 HIS 0.002 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 4302) covalent geometry : angle 0.48214 ( 5857) SS BOND : bond 0.00080 ( 2) SS BOND : angle 1.59247 ( 4) hydrogen bonds : bond 0.04424 ( 259) hydrogen bonds : angle 3.95845 ( 726) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: A 200 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.8761 (t80) outliers start: 7 outliers final: 4 residues processed: 55 average time/residue: 0.9279 time to fit residues: 53.6537 Evaluate side-chains 53 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 520 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 9 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 0.0050 chunk 20 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.105263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.085764 restraints weight = 21063.174| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.37 r_work: 0.2879 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4304 Z= 0.110 Angle : 0.477 5.581 5861 Z= 0.247 Chirality : 0.037 0.177 673 Planarity : 0.003 0.027 726 Dihedral : 3.401 17.284 575 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.44 % Allowed : 17.43 % Favored : 82.14 % 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: 2.33 (0.37), residues: 526 helix: 2.10 (0.28), residues: 339 sheet: None (None), residues: 0 loop : 0.63 (0.48), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 488 TYR 0.007 0.001 TYR A 239 PHE 0.010 0.001 PHE A 34 TRP 0.012 0.001 TRP A 62 HIS 0.001 0.000 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 4302) covalent geometry : angle 0.47571 ( 5857) SS BOND : bond 0.00038 ( 2) SS BOND : angle 1.55775 ( 4) hydrogen bonds : bond 0.04141 ( 259) hydrogen bonds : angle 3.89209 ( 726) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 PHE cc_start: 0.9098 (OUTLIER) cc_final: 0.8789 (t80) REVERT: A 271 VAL cc_start: 0.8321 (t) cc_final: 0.8098 (p) outliers start: 2 outliers final: 0 residues processed: 54 average time/residue: 0.9659 time to fit residues: 54.7487 Evaluate side-chains 50 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 0.3980 chunk 3 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.104945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.085536 restraints weight = 21326.017| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.36 r_work: 0.2885 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4304 Z= 0.117 Angle : 0.477 5.584 5861 Z= 0.246 Chirality : 0.037 0.183 673 Planarity : 0.003 0.028 726 Dihedral : 3.378 17.297 575 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.87 % Allowed : 16.99 % Favored : 82.14 % 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: 2.33 (0.37), residues: 526 helix: 2.12 (0.28), residues: 338 sheet: None (None), residues: 0 loop : 0.60 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 488 TYR 0.007 0.001 TYR A 447 PHE 0.011 0.001 PHE A 34 TRP 0.017 0.001 TRP A 62 HIS 0.001 0.000 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 4302) covalent geometry : angle 0.47496 ( 5857) SS BOND : bond 0.00050 ( 2) SS BOND : angle 1.57866 ( 4) hydrogen bonds : bond 0.04186 ( 259) hydrogen bonds : angle 3.89649 ( 726) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 PHE cc_start: 0.9110 (OUTLIER) cc_final: 0.8885 (t80) REVERT: A 210 ASN cc_start: 0.9004 (OUTLIER) cc_final: 0.8745 (p0) outliers start: 4 outliers final: 1 residues processed: 54 average time/residue: 0.9246 time to fit residues: 52.4172 Evaluate side-chains 53 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 347 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 16 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 3 optimal weight: 0.0170 chunk 28 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.104604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.084948 restraints weight = 21153.524| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.39 r_work: 0.2892 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4304 Z= 0.108 Angle : 0.472 5.560 5861 Z= 0.244 Chirality : 0.037 0.180 673 Planarity : 0.003 0.027 726 Dihedral : 3.350 17.323 575 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.87 % Allowed : 16.99 % Favored : 82.14 % 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: 2.44 (0.38), residues: 526 helix: 2.19 (0.28), residues: 339 sheet: None (None), residues: 0 loop : 0.67 (0.48), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 488 TYR 0.007 0.001 TYR A 239 PHE 0.010 0.001 PHE A 34 TRP 0.016 0.001 TRP A 62 HIS 0.001 0.000 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 4302) covalent geometry : angle 0.47055 ( 5857) SS BOND : bond 0.00032 ( 2) SS BOND : angle 1.55062 ( 4) hydrogen bonds : bond 0.04045 ( 259) hydrogen bonds : angle 3.86242 ( 726) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2812.66 seconds wall clock time: 48 minutes 16.87 seconds (2896.87 seconds total)