Starting phenix.real_space_refine on Tue Mar 3 11:17:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n5g_24189/03_2026/7n5g_24189.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n5g_24189/03_2026/7n5g_24189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n5g_24189/03_2026/7n5g_24189.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n5g_24189/03_2026/7n5g_24189.map" model { file = "/net/cci-nas-00/data/ceres_data/7n5g_24189/03_2026/7n5g_24189.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n5g_24189/03_2026/7n5g_24189.cif" } resolution = 2.4 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= 0.001 sd= 0.023 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: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 1920 2.51 5 N 486 2.21 5 O 508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2926 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2908 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 363} Chain breaks: 4 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 3, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.86, per 1000 atoms: 0.29 Number of scatterers: 2926 At special positions: 0 Unit cell: (70.04, 93.73, 140.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 508 8.00 N 486 7.00 C 1920 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.28 Conformation dependent library (CDL) restraints added in 116.1 milliseconds 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 720 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 2 sheets defined 63.9% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'B' and resid 186 through 203 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 235 through 241 Processing helix chain 'B' and resid 265 through 285 Processing helix chain 'B' and resid 295 through 329 removed outlier: 3.824A pdb=" N LEU B 299 " --> pdb=" O THR B 295 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER B 329 " --> pdb=" O ILE B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 331 No H-bonds generated for 'chain 'B' and resid 330 through 331' Processing helix chain 'B' and resid 332 through 334 No H-bonds generated for 'chain 'B' and resid 332 through 334' Processing helix chain 'B' and resid 335 through 349 Processing helix chain 'B' and resid 508 through 524 Processing helix chain 'B' and resid 526 through 552 Processing helix chain 'B' and resid 556 through 590 removed outlier: 5.467A pdb=" N ASN B 576 " --> pdb=" O PHE B 572 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N THR B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 635 Processing helix chain 'B' and resid 661 through 678 Processing helix chain 'B' and resid 714 through 737 Processing sheet with id=AA1, first strand: chain 'B' and resid 626 through 630 removed outlier: 7.157A pdb=" N THR B 616 " --> pdb=" O MET B 612 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N MET B 612 " --> pdb=" O THR B 616 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL B 618 " --> pdb=" O GLU B 610 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 649 through 657 removed outlier: 6.485A pdb=" N LYS B 699 " --> pdb=" O ILE B 694 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE B 694 " --> pdb=" O LYS B 699 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LYS B 701 " --> pdb=" O LYS B 692 " (cutoff:3.500A) 206 hydrogen bonds defined for protein. 612 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: 0.54 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 675 1.32 - 1.44: 718 1.44 - 1.57: 1550 1.57 - 1.69: 16 1.69 - 1.81: 21 Bond restraints: 2980 Sorted by residual: bond pdb=" CD2 TRP B 507 " pdb=" CE3 TRP B 507 " ideal model delta sigma weight residual 1.398 1.503 -0.105 1.60e-02 3.91e+03 4.27e+01 bond pdb=" CZ2 TRP B 507 " pdb=" CH2 TRP B 507 " ideal model delta sigma weight residual 1.368 1.480 -0.112 1.90e-02 2.77e+03 3.46e+01 bond pdb=" CB ILE B 285 " pdb=" CG1 ILE B 285 " ideal model delta sigma weight residual 1.530 1.635 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" CB TYR B 629 " pdb=" CG TYR B 629 " ideal model delta sigma weight residual 1.512 1.399 0.113 2.20e-02 2.07e+03 2.65e+01 bond pdb=" CB HIS B 345 " pdb=" CG HIS B 345 " ideal model delta sigma weight residual 1.497 1.428 0.069 1.40e-02 5.10e+03 2.46e+01 ... (remaining 2975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 3160 1.65 - 3.30: 695 3.30 - 4.95: 146 4.95 - 6.59: 33 6.59 - 8.24: 5 Bond angle restraints: 4039 Sorted by residual: angle pdb=" C HIS B 592 " pdb=" N PRO B 593 " pdb=" CA PRO B 593 " ideal model delta sigma weight residual 119.56 126.54 -6.98 1.01e+00 9.80e-01 4.78e+01 angle pdb=" C SER B 645 " pdb=" N PRO B 646 " pdb=" CA PRO B 646 " ideal model delta sigma weight residual 120.52 126.91 -6.39 9.90e-01 1.02e+00 4.17e+01 angle pdb=" C LEU B 743 " pdb=" N PRO B 744 " pdb=" CA PRO B 744 " ideal model delta sigma weight residual 119.85 126.24 -6.39 1.01e+00 9.80e-01 4.00e+01 angle pdb=" C GLN B 291 " pdb=" N PRO B 292 " pdb=" CA PRO B 292 " ideal model delta sigma weight residual 119.28 125.41 -6.13 1.10e+00 8.26e-01 3.11e+01 angle pdb=" N SER B 267 " pdb=" CA SER B 267 " pdb=" C SER B 267 " ideal model delta sigma weight residual 112.23 105.58 6.65 1.26e+00 6.30e-01 2.79e+01 ... (remaining 4034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.33: 1685 14.33 - 28.65: 62 28.65 - 42.97: 7 42.97 - 57.30: 11 57.30 - 71.62: 6 Dihedral angle restraints: 1771 sinusoidal: 680 harmonic: 1091 Sorted by residual: dihedral pdb=" CA ASP B 657 " pdb=" CB ASP B 657 " pdb=" CG ASP B 657 " pdb=" OD1 ASP B 657 " ideal model delta sinusoidal sigma weight residual -30.00 -84.87 54.87 1 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CA ASP B 595 " pdb=" CB ASP B 595 " pdb=" CG ASP B 595 " pdb=" OD1 ASP B 595 " ideal model delta sinusoidal sigma weight residual -30.00 -74.43 44.43 1 2.00e+01 2.50e-03 6.86e+00 dihedral pdb=" N ASP B 650 " pdb=" C ASP B 650 " pdb=" CA ASP B 650 " pdb=" CB ASP B 650 " ideal model delta harmonic sigma weight residual 122.80 116.39 6.41 0 2.50e+00 1.60e-01 6.57e+00 ... (remaining 1768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 371 0.097 - 0.193: 99 0.193 - 0.290: 16 0.290 - 0.387: 3 0.387 - 0.483: 2 Chirality restraints: 491 Sorted by residual: chirality pdb=" CG LEU B 264 " pdb=" CB LEU B 264 " pdb=" CD1 LEU B 264 " pdb=" CD2 LEU B 264 " both_signs ideal model delta sigma weight residual False -2.59 -3.07 0.48 2.00e-01 2.50e+01 5.84e+00 chirality pdb=" CB ILE B 285 " pdb=" CA ILE B 285 " pdb=" CG1 ILE B 285 " pdb=" CG2 ILE B 285 " both_signs ideal model delta sigma weight residual False 2.64 3.05 -0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" CA TRP B 304 " pdb=" N TRP B 304 " pdb=" C TRP B 304 " pdb=" CB TRP B 304 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.19e+00 ... (remaining 488 not shown) Planarity restraints: 493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 697 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.41e+00 pdb=" C VAL B 697 " -0.053 2.00e-02 2.50e+03 pdb=" O VAL B 697 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN B 698 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 675 " 0.035 2.00e-02 2.50e+03 1.98e-02 7.85e+00 pdb=" CG TYR B 675 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR B 675 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B 675 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 675 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR B 675 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR B 675 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 675 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 741 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.86e+00 pdb=" C ASN B 741 " 0.042 2.00e-02 2.50e+03 pdb=" O ASN B 741 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU B 742 " -0.014 2.00e-02 2.50e+03 ... (remaining 490 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1125 2.89 - 3.39: 2994 3.39 - 3.89: 4759 3.89 - 4.40: 5429 4.40 - 4.90: 8451 Nonbonded interactions: 22758 Sorted by model distance: nonbonded pdb=" OD1 ASP B 737 " pdb=" NZ LYS B 739 " model vdw 2.386 3.120 nonbonded pdb=" N VAL B 697 " pdb=" N ASN B 698 " model vdw 2.467 2.560 nonbonded pdb=" N ASN B 711 " pdb=" O ASN B 711 " model vdw 2.498 2.496 nonbonded pdb=" N PRO B 646 " pdb=" O PRO B 646 " model vdw 2.533 2.496 nonbonded pdb=" N ASN B 613 " pdb=" O ASN B 613 " model vdw 2.553 2.496 ... (remaining 22753 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: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.950 Find NCS groups from input model: 0.010 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:7.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 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 : 0.022 0.132 2980 Z= 1.192 Angle : 1.511 8.243 4039 Z= 1.034 Chirality : 0.093 0.483 491 Planarity : 0.008 0.031 493 Dihedral : 10.569 71.622 1051 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 0.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.84 (0.41), residues: 361 helix: 1.41 (0.30), residues: 223 sheet: 0.94 (0.88), residues: 42 loop : 1.21 (0.65), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 338 TYR 0.035 0.008 TYR B 675 PHE 0.019 0.005 PHE B 682 TRP 0.028 0.008 TRP B 683 HIS 0.005 0.002 HIS B 346 Details of bonding type rmsd covalent geometry : bond 0.02231 ( 2980) covalent geometry : angle 1.51055 ( 4039) hydrogen bonds : bond 0.14388 ( 206) hydrogen bonds : angle 5.83451 ( 612) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.121 Fit side-chains revert: symmetry clash REVERT: B 526 LYS cc_start: 0.7984 (mttt) cc_final: 0.7595 (mtpp) REVERT: B 624 LYS cc_start: 0.8434 (mmtm) cc_final: 0.7572 (tttp) REVERT: B 702 MET cc_start: 0.8860 (mtt) cc_final: 0.8638 (mtp) outliers start: 0 outliers final: 1 residues processed: 99 average time/residue: 0.5263 time to fit residues: 53.3404 Evaluate side-chains 85 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 560 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.0970 chunk 19 optimal weight: 0.1980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN B 605 ASN B 648 GLN B 688 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.160918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.133786 restraints weight = 4039.146| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 1.69 r_work: 0.3742 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2980 Z= 0.138 Angle : 0.483 5.856 4039 Z= 0.263 Chirality : 0.040 0.143 491 Planarity : 0.003 0.038 493 Dihedral : 8.411 56.527 397 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 4.23 % Allowed : 9.45 % Favored : 86.32 % 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: 2.82 (0.43), residues: 361 helix: 2.56 (0.32), residues: 229 sheet: 0.49 (0.76), residues: 42 loop : 0.83 (0.68), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 720 TYR 0.005 0.001 TYR B 629 PHE 0.009 0.001 PHE B 594 TRP 0.013 0.002 TRP B 281 HIS 0.003 0.001 HIS B 708 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 2980) covalent geometry : angle 0.48341 ( 4039) hydrogen bonds : bond 0.05460 ( 206) hydrogen bonds : angle 3.91278 ( 612) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.107 Fit side-chains revert: symmetry clash REVERT: B 283 MET cc_start: 0.5732 (tpp) cc_final: 0.5427 (mmm) REVERT: B 623 ASP cc_start: 0.8253 (p0) cc_final: 0.7967 (p0) outliers start: 13 outliers final: 6 residues processed: 95 average time/residue: 0.5480 time to fit residues: 53.1976 Evaluate side-chains 89 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 562 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 16 optimal weight: 0.5980 chunk 4 optimal weight: 0.0980 chunk 1 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.160318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.133601 restraints weight = 4065.294| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 1.66 r_work: 0.3735 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2980 Z= 0.131 Angle : 0.447 7.022 4039 Z= 0.237 Chirality : 0.039 0.139 491 Planarity : 0.003 0.029 493 Dihedral : 8.099 56.609 397 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.93 % Allowed : 13.36 % Favored : 83.71 % 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: 3.09 (0.43), residues: 361 helix: 2.88 (0.32), residues: 229 sheet: 0.58 (0.76), residues: 42 loop : 0.60 (0.68), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 720 TYR 0.008 0.001 TYR B 740 PHE 0.012 0.002 PHE B 594 TRP 0.013 0.002 TRP B 548 HIS 0.003 0.001 HIS B 708 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 2980) covalent geometry : angle 0.44707 ( 4039) hydrogen bonds : bond 0.04606 ( 206) hydrogen bonds : angle 3.61256 ( 612) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.090 Fit side-chains revert: symmetry clash REVERT: B 624 LYS cc_start: 0.8730 (mmtm) cc_final: 0.7641 (tmmt) REVERT: B 734 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7858 (mt-10) REVERT: B 737 ASP cc_start: 0.7844 (t0) cc_final: 0.7565 (t0) outliers start: 9 outliers final: 6 residues processed: 91 average time/residue: 0.5296 time to fit residues: 49.3268 Evaluate side-chains 88 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 718 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 7 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 0.0870 chunk 10 optimal weight: 0.8980 chunk 22 optimal weight: 0.0770 chunk 16 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN B 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.161259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.134559 restraints weight = 4091.103| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.68 r_work: 0.3753 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3618 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2980 Z= 0.098 Angle : 0.403 7.239 4039 Z= 0.210 Chirality : 0.038 0.134 491 Planarity : 0.002 0.027 493 Dihedral : 7.713 53.996 397 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 4.23 % Allowed : 14.98 % Favored : 80.78 % 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: 3.39 (0.43), residues: 361 helix: 3.18 (0.32), residues: 229 sheet: 0.72 (0.79), residues: 42 loop : 0.50 (0.67), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 720 TYR 0.007 0.001 TYR B 740 PHE 0.010 0.001 PHE B 654 TRP 0.009 0.001 TRP B 548 HIS 0.002 0.000 HIS B 708 Details of bonding type rmsd covalent geometry : bond 0.00195 ( 2980) covalent geometry : angle 0.40309 ( 4039) hydrogen bonds : bond 0.03945 ( 206) hydrogen bonds : angle 3.34870 ( 612) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.099 Fit side-chains REVERT: B 624 LYS cc_start: 0.8772 (mmtm) cc_final: 0.7665 (tmmt) REVERT: B 692 LYS cc_start: 0.8604 (mtmt) cc_final: 0.8255 (mtmt) REVERT: B 737 ASP cc_start: 0.7765 (t0) cc_final: 0.7416 (t0) outliers start: 13 outliers final: 6 residues processed: 91 average time/residue: 0.5001 time to fit residues: 46.5301 Evaluate side-chains 95 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 678 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 35 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 8 optimal weight: 0.0980 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 0.0670 chunk 27 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN B 713 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.161098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.134345 restraints weight = 4000.376| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 1.65 r_work: 0.3749 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3615 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2980 Z= 0.104 Angle : 0.426 7.702 4039 Z= 0.220 Chirality : 0.039 0.140 491 Planarity : 0.002 0.027 493 Dihedral : 7.370 56.099 395 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 4.23 % Allowed : 14.66 % Favored : 81.11 % 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: 3.43 (0.43), residues: 361 helix: 3.27 (0.32), residues: 229 sheet: 0.70 (0.78), residues: 42 loop : 0.34 (0.66), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 720 TYR 0.006 0.001 TYR B 740 PHE 0.010 0.001 PHE B 654 TRP 0.008 0.001 TRP B 548 HIS 0.003 0.001 HIS B 708 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 2980) covalent geometry : angle 0.42636 ( 4039) hydrogen bonds : bond 0.03938 ( 206) hydrogen bonds : angle 3.34915 ( 612) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.105 Fit side-chains REVERT: B 294 GLN cc_start: 0.7276 (tt0) cc_final: 0.6678 (pm20) REVERT: B 623 ASP cc_start: 0.8364 (p0) cc_final: 0.8124 (p0) REVERT: B 624 LYS cc_start: 0.8792 (mmtm) cc_final: 0.7777 (tmmt) REVERT: B 692 LYS cc_start: 0.8586 (mtmt) cc_final: 0.8157 (mtmt) REVERT: B 713 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7944 (mm-40) REVERT: B 718 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8112 (ptmm) REVERT: B 728 GLU cc_start: 0.8290 (tp30) cc_final: 0.7967 (tp30) REVERT: B 731 LYS cc_start: 0.8693 (ttpm) cc_final: 0.8285 (ttpp) REVERT: B 737 ASP cc_start: 0.7766 (t0) cc_final: 0.7406 (t0) outliers start: 13 outliers final: 7 residues processed: 91 average time/residue: 0.5481 time to fit residues: 51.0125 Evaluate side-chains 92 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 678 GLN Chi-restraints excluded: chain B residue 713 GLN Chi-restraints excluded: chain B residue 718 LYS Chi-restraints excluded: chain B residue 739 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 29 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN B 531 GLN B 648 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.159989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.133102 restraints weight = 3982.030| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 1.65 r_work: 0.3732 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3596 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2980 Z= 0.145 Angle : 0.459 7.453 4039 Z= 0.237 Chirality : 0.040 0.153 491 Planarity : 0.002 0.028 493 Dihedral : 7.426 59.237 395 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.58 % Allowed : 16.29 % Favored : 80.13 % 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: 3.35 (0.44), residues: 361 helix: 3.22 (0.32), residues: 229 sheet: 0.62 (0.79), residues: 42 loop : 0.29 (0.67), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 720 TYR 0.007 0.001 TYR B 740 PHE 0.011 0.001 PHE B 271 TRP 0.011 0.001 TRP B 548 HIS 0.004 0.001 HIS B 708 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 2980) covalent geometry : angle 0.45854 ( 4039) hydrogen bonds : bond 0.04339 ( 206) hydrogen bonds : angle 3.50499 ( 612) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.082 Fit side-chains revert: symmetry clash REVERT: B 623 ASP cc_start: 0.8366 (p0) cc_final: 0.8108 (p0) REVERT: B 624 LYS cc_start: 0.8786 (mmtm) cc_final: 0.7805 (tmmt) REVERT: B 692 LYS cc_start: 0.8623 (mtmt) cc_final: 0.8202 (mtmt) REVERT: B 718 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8201 (ptmt) REVERT: B 731 LYS cc_start: 0.8706 (ttpm) cc_final: 0.8326 (ttpp) outliers start: 11 outliers final: 7 residues processed: 90 average time/residue: 0.5339 time to fit residues: 49.1602 Evaluate side-chains 93 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 718 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN B 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.159300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.132322 restraints weight = 4094.555| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 1.67 r_work: 0.3715 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2980 Z= 0.147 Angle : 0.463 7.979 4039 Z= 0.238 Chirality : 0.040 0.147 491 Planarity : 0.002 0.028 493 Dihedral : 7.298 58.796 395 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.91 % Allowed : 15.31 % Favored : 80.78 % 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: 3.28 (0.44), residues: 361 helix: 3.19 (0.32), residues: 229 sheet: 0.48 (0.79), residues: 42 loop : 0.26 (0.67), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 720 TYR 0.007 0.001 TYR B 740 PHE 0.012 0.001 PHE B 654 TRP 0.013 0.001 TRP B 548 HIS 0.004 0.001 HIS B 708 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 2980) covalent geometry : angle 0.46346 ( 4039) hydrogen bonds : bond 0.04540 ( 206) hydrogen bonds : angle 3.61242 ( 612) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.111 Fit side-chains REVERT: B 623 ASP cc_start: 0.8387 (p0) cc_final: 0.8158 (p0) REVERT: B 624 LYS cc_start: 0.8801 (mmtm) cc_final: 0.7861 (tmmt) REVERT: B 737 ASP cc_start: 0.7801 (t0) cc_final: 0.7433 (t0) outliers start: 12 outliers final: 7 residues processed: 92 average time/residue: 0.5169 time to fit residues: 48.6703 Evaluate side-chains 94 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 662 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 chunk 30 optimal weight: 0.0870 chunk 3 optimal weight: 5.9990 chunk 21 optimal weight: 0.0060 chunk 4 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 overall best weight: 0.3974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN B 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.161382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.134125 restraints weight = 4079.749| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 1.69 r_work: 0.3743 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2980 Z= 0.102 Angle : 0.438 8.470 4039 Z= 0.225 Chirality : 0.039 0.148 491 Planarity : 0.002 0.027 493 Dihedral : 7.183 59.611 395 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 4.23 % Allowed : 15.64 % Favored : 80.13 % 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: 3.40 (0.44), residues: 361 helix: 3.31 (0.32), residues: 229 sheet: 0.48 (0.79), residues: 42 loop : 0.24 (0.68), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 296 TYR 0.007 0.001 TYR B 740 PHE 0.010 0.001 PHE B 572 TRP 0.011 0.001 TRP B 548 HIS 0.003 0.001 HIS B 708 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 2980) covalent geometry : angle 0.43778 ( 4039) hydrogen bonds : bond 0.03979 ( 206) hydrogen bonds : angle 3.53009 ( 612) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.079 Fit side-chains REVERT: B 623 ASP cc_start: 0.8375 (p0) cc_final: 0.8163 (p0) REVERT: B 624 LYS cc_start: 0.8823 (mmtm) cc_final: 0.7843 (tmmt) REVERT: B 737 ASP cc_start: 0.7709 (t0) cc_final: 0.7342 (t0) outliers start: 13 outliers final: 8 residues processed: 93 average time/residue: 0.4909 time to fit residues: 46.7531 Evaluate side-chains 94 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 678 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN B 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.160098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.133070 restraints weight = 4069.657| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 1.67 r_work: 0.3725 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2980 Z= 0.144 Angle : 0.537 11.841 4039 Z= 0.276 Chirality : 0.040 0.155 491 Planarity : 0.002 0.028 493 Dihedral : 7.240 58.081 395 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.61 % Allowed : 17.92 % Favored : 79.48 % 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: 3.30 (0.44), residues: 361 helix: 3.22 (0.33), residues: 229 sheet: 0.49 (0.80), residues: 42 loop : 0.24 (0.68), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 720 TYR 0.007 0.001 TYR B 740 PHE 0.010 0.001 PHE B 572 TRP 0.010 0.001 TRP B 548 HIS 0.004 0.001 HIS B 708 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 2980) covalent geometry : angle 0.53723 ( 4039) hydrogen bonds : bond 0.04441 ( 206) hydrogen bonds : angle 3.67512 ( 612) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.130 Fit side-chains REVERT: B 623 ASP cc_start: 0.8392 (p0) cc_final: 0.8157 (p0) REVERT: B 624 LYS cc_start: 0.8823 (mmtm) cc_final: 0.7867 (tmmt) REVERT: B 737 ASP cc_start: 0.7699 (t0) cc_final: 0.7337 (t0) outliers start: 8 outliers final: 6 residues processed: 90 average time/residue: 0.5344 time to fit residues: 49.2825 Evaluate side-chains 92 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 662 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 21 optimal weight: 0.0040 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 0.0060 chunk 18 optimal weight: 0.8980 chunk 36 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 overall best weight: 0.3408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN B 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.161595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.134706 restraints weight = 4020.216| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.67 r_work: 0.3752 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 2980 Z= 0.112 Angle : 0.512 10.899 4039 Z= 0.262 Chirality : 0.039 0.129 491 Planarity : 0.002 0.027 493 Dihedral : 7.222 57.884 395 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.28 % Allowed : 17.26 % Favored : 80.46 % 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: 3.38 (0.45), residues: 361 helix: 3.29 (0.33), residues: 229 sheet: 0.53 (0.81), residues: 42 loop : 0.25 (0.68), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 671 TYR 0.006 0.001 TYR B 740 PHE 0.011 0.001 PHE B 572 TRP 0.007 0.001 TRP B 548 HIS 0.002 0.000 HIS B 708 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 2980) covalent geometry : angle 0.51157 ( 4039) hydrogen bonds : bond 0.03990 ( 206) hydrogen bonds : angle 3.58728 ( 612) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.082 Fit side-chains REVERT: B 623 ASP cc_start: 0.8365 (p0) cc_final: 0.8143 (p0) REVERT: B 624 LYS cc_start: 0.8817 (mmtm) cc_final: 0.7848 (tmmt) REVERT: B 737 ASP cc_start: 0.7697 (t0) cc_final: 0.7338 (t0) outliers start: 7 outliers final: 5 residues processed: 93 average time/residue: 0.5053 time to fit residues: 48.0940 Evaluate side-chains 94 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 662 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.0070 chunk 32 optimal weight: 0.9990 chunk 13 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 523 ASN B 525 ASN B 531 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.160470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.133819 restraints weight = 4010.310| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 1.58 r_work: 0.3740 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2980 Z= 0.141 Angle : 0.542 10.464 4039 Z= 0.275 Chirality : 0.040 0.129 491 Planarity : 0.002 0.028 493 Dihedral : 7.314 57.067 395 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.95 % Allowed : 18.24 % Favored : 79.80 % 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: 3.36 (0.45), residues: 361 helix: 3.26 (0.33), residues: 229 sheet: 0.48 (0.81), residues: 42 loop : 0.27 (0.69), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 720 TYR 0.007 0.001 TYR B 740 PHE 0.010 0.001 PHE B 715 TRP 0.009 0.001 TRP B 548 HIS 0.004 0.001 HIS B 708 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 2980) covalent geometry : angle 0.54166 ( 4039) hydrogen bonds : bond 0.04387 ( 206) hydrogen bonds : angle 3.65172 ( 612) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2195.98 seconds wall clock time: 37 minutes 57.39 seconds (2277.39 seconds total)