Starting phenix.real_space_refine on Wed Jul 1 21:37:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w3f_65599/07_2026/9w3f_65599.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w3f_65599/07_2026/9w3f_65599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w3f_65599/07_2026/9w3f_65599.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w3f_65599/07_2026/9w3f_65599.map" model { file = "/net/cci-nas-00/data/ceres_data/9w3f_65599/07_2026/9w3f_65599.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w3f_65599/07_2026/9w3f_65599.cif" } resolution = 3.04 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= 0.108 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 22 5.16 5 C 1969 2.51 5 N 485 2.21 5 O 517 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2993 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2150 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 7, 'TRANS': 267} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 817 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 1, 'TRANS': 116} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'BER': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 0.99, per 1000 atoms: 0.33 Number of scatterers: 2993 At special positions: 0 Unit cell: (54.944, 58.176, 107.464, 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 22 16.00 O 517 8.00 N 485 7.00 C 1969 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 106 " - pdb=" SG CYS A 191 " distance=2.03 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 190 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " 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: 0.29 Conformation dependent library (CDL) restraints added in 122.0 milliseconds 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 736 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 3 sheets defined 62.6% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 31 through 61 removed outlier: 3.762A pdb=" N ILE A 55 " --> pdb=" O ASN A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 86 Processing helix chain 'A' and resid 86 through 97 Processing helix chain 'A' and resid 101 through 136 removed outlier: 4.167A pdb=" N TRP A 105 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR A 136 " --> pdb=" O TYR A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 171 removed outlier: 3.619A pdb=" N LEU A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 178 through 187 Processing helix chain 'A' and resid 196 through 207 Processing helix chain 'A' and resid 208 through 228 Processing helix chain 'A' and resid 267 through 295 Proline residue: A 288 - end of helix Processing helix chain 'A' and resid 296 through 298 No H-bonds generated for 'chain 'A' and resid 296 through 298' Processing helix chain 'A' and resid 304 through 318 removed outlier: 3.932A pdb=" N TYR A 308 " --> pdb=" O ARG A 304 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN A 318 " --> pdb=" O ILE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 327 removed outlier: 4.167A pdb=" N LEU A 324 " --> pdb=" O GLY A 320 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N CYS A 327 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 341 Processing helix chain 'B' and resid 61 through 64 Processing helix chain 'B' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 7 Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.676A pdb=" N ASN B 96 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP B 33 " --> pdb=" O LYS B 98 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 13 218 hydrogen bonds defined for protein. 624 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: 0.46 Time building geometry restraints manager: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 909 1.34 - 1.46: 800 1.46 - 1.58: 1324 1.58 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 3065 Sorted by residual: bond pdb=" C18 BER A1201 " pdb=" O4 BER A1201 " ideal model delta sigma weight residual 1.335 1.402 -0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C11 BER A1201 " pdb=" C5 BER A1201 " ideal model delta sigma weight residual 1.366 1.432 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" C14 BER A1201 " pdb=" O2 BER A1201 " ideal model delta sigma weight residual 1.346 1.410 -0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C14 BER A1201 " pdb=" C9 BER A1201 " ideal model delta sigma weight residual 1.372 1.432 -0.060 2.00e-02 2.50e+03 8.91e+00 bond pdb=" C11 BER A1201 " pdb=" O1 BER A1201 " ideal model delta sigma weight residual 1.352 1.410 -0.058 2.00e-02 2.50e+03 8.36e+00 ... (remaining 3060 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 4097 1.44 - 2.88: 62 2.88 - 4.31: 17 4.31 - 5.75: 7 5.75 - 7.19: 1 Bond angle restraints: 4184 Sorted by residual: angle pdb=" C2 BER A1201 " pdb=" C1 BER A1201 " pdb=" C3 BER A1201 " ideal model delta sigma weight residual 123.81 116.62 7.19 3.00e+00 1.11e-01 5.74e+00 angle pdb=" N GLY B 35 " pdb=" CA GLY B 35 " pdb=" C GLY B 35 " ideal model delta sigma weight residual 111.12 114.41 -3.29 1.49e+00 4.50e-01 4.88e+00 angle pdb=" C ILE B 28 " pdb=" N PHE B 29 " pdb=" CA PHE B 29 " ideal model delta sigma weight residual 121.54 125.68 -4.14 1.91e+00 2.74e-01 4.70e+00 angle pdb=" C VAL A 292 " pdb=" CA VAL A 292 " pdb=" CB VAL A 292 " ideal model delta sigma weight residual 112.14 109.27 2.87 1.35e+00 5.49e-01 4.51e+00 angle pdb=" N SER B 30 " pdb=" CA SER B 30 " pdb=" C SER B 30 " ideal model delta sigma weight residual 113.28 110.70 2.58 1.22e+00 6.72e-01 4.46e+00 ... (remaining 4179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.12: 1473 15.12 - 30.23: 210 30.23 - 45.35: 62 45.35 - 60.47: 14 60.47 - 75.59: 2 Dihedral angle restraints: 1761 sinusoidal: 618 harmonic: 1143 Sorted by residual: dihedral pdb=" CA ASN A 51 " pdb=" C ASN A 51 " pdb=" N VAL A 52 " pdb=" CA VAL A 52 " ideal model delta harmonic sigma weight residual 180.00 164.39 15.61 0 5.00e+00 4.00e-02 9.75e+00 dihedral pdb=" CB LYS A 267 " pdb=" CG LYS A 267 " pdb=" CD LYS A 267 " pdb=" CE LYS A 267 " ideal model delta sinusoidal sigma weight residual 60.00 1.90 58.10 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA LYS B 98 " pdb=" CB LYS B 98 " pdb=" CG LYS B 98 " pdb=" CD LYS B 98 " ideal model delta sinusoidal sigma weight residual 180.00 -122.14 -57.86 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 1758 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 275 0.025 - 0.049: 114 0.049 - 0.073: 75 0.073 - 0.098: 24 0.098 - 0.122: 9 Chirality restraints: 497 Sorted by residual: chirality pdb=" CA THR A 177 " pdb=" N THR A 177 " pdb=" C THR A 177 " pdb=" CB THR A 177 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.12 2.00e-01 2.50e+01 3.74e-01 chirality pdb=" CA ILE B 105 " pdb=" N ILE B 105 " pdb=" C ILE B 105 " pdb=" CB ILE B 105 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.33e-01 chirality pdb=" CA VAL B 115 " pdb=" N VAL B 115 " pdb=" C VAL B 115 " pdb=" CB VAL B 115 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.22e-01 ... (remaining 494 not shown) Planarity restraints: 506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 40 " 0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO B 41 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 41 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 41 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 130 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.31e+00 pdb=" CG ASP A 130 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASP A 130 " -0.007 2.00e-02 2.50e+03 pdb=" OD2 ASP A 130 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 29 " 0.005 2.00e-02 2.50e+03 7.96e-03 1.11e+00 pdb=" CG PHE B 29 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE B 29 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 29 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 29 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 29 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 29 " -0.001 2.00e-02 2.50e+03 ... (remaining 503 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 253 2.74 - 3.28: 2947 3.28 - 3.82: 5184 3.82 - 4.36: 5646 4.36 - 4.90: 10412 Nonbonded interactions: 24442 Sorted by model distance: nonbonded pdb=" C5 BER A1201 " pdb=" O HOH A1301 " model vdw 2.201 3.340 nonbonded pdb=" OD2 ASP A 113 " pdb=" OH TYR A 316 " model vdw 2.207 3.040 nonbonded pdb=" OE2 GLU A 268 " pdb=" OH TYR B 106 " model vdw 2.219 3.040 nonbonded pdb=" O ASN B 32 " pdb=" NH2 ARG B 71 " model vdw 2.223 3.120 nonbonded pdb=" OH TYR A 185 " pdb=" O PHE A 194 " model vdw 2.268 3.040 ... (remaining 24437 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 5.050 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 3068 Z= 0.215 Angle : 0.522 7.188 4190 Z= 0.273 Chirality : 0.039 0.122 497 Planarity : 0.003 0.035 506 Dihedral : 15.809 75.586 1016 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 24.33 % Favored : 75.67 % 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: 1.35 (0.46), residues: 387 helix: 2.40 (0.34), residues: 224 sheet: -1.82 (0.68), residues: 58 loop : -0.76 (0.67), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 19 TYR 0.009 0.001 TYR A 219 PHE 0.018 0.001 PHE B 29 TRP 0.011 0.001 TRP A 313 HIS 0.006 0.002 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.22 ( 3065) covalent geometry : angle 0.52200 / 0.27 ( 4184) SS BOND : bond 0.00141 / 0.07 ( 3) SS BOND : angle 0.39168 / 0.22 ( 6) hydrogen bonds : bond 0.10181 / 6.52 ( 210) hydrogen bonds : angle 5.57359 / 4.08 ( 624) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.108 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0463 time to fit residues: 1.7398 Evaluate side-chains 26 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.153780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.108645 restraints weight = 3107.713| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.58 r_work: 0.3126 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.0453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3068 Z= 0.131 Angle : 0.449 5.385 4190 Z= 0.245 Chirality : 0.039 0.129 497 Planarity : 0.003 0.029 506 Dihedral : 3.973 17.208 433 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.67 % Allowed : 23.00 % Favored : 74.33 % 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: 1.40 (0.45), residues: 387 helix: 2.46 (0.34), residues: 224 sheet: -1.74 (0.71), residues: 52 loop : -0.93 (0.61), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 71 TYR 0.010 0.001 TYR A 219 PHE 0.006 0.001 PHE A 49 TRP 0.009 0.001 TRP A 313 HIS 0.005 0.001 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 3065) covalent geometry : angle 0.44899 / 0.24 ( 4184) SS BOND : bond 0.00132 / 0.06 ( 3) SS BOND : angle 0.43656 / 0.25 ( 6) hydrogen bonds : bond 0.03406 / 2.37 ( 210) hydrogen bonds : angle 4.30748 / 3.17 ( 624) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.102 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 30 average time/residue: 0.0395 time to fit residues: 1.7085 Evaluate side-chains 34 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 56 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 14 optimal weight: 0.0470 chunk 0 optimal weight: 6.9990 chunk 3 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 chunk 2 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.156030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.110961 restraints weight = 3068.176| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.57 r_work: 0.3039 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.0623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3068 Z= 0.099 Angle : 0.417 5.293 4190 Z= 0.227 Chirality : 0.038 0.127 497 Planarity : 0.003 0.028 506 Dihedral : 3.737 15.796 433 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.33 % Allowed : 23.67 % Favored : 74.00 % 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: 1.57 (0.45), residues: 387 helix: 2.59 (0.35), residues: 224 sheet: -1.37 (0.67), residues: 58 loop : -0.97 (0.64), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 71 TYR 0.010 0.001 TYR A 219 PHE 0.006 0.001 PHE A 49 TRP 0.010 0.001 TRP A 313 HIS 0.004 0.001 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 3065) covalent geometry : angle 0.41741 / 0.23 ( 4184) SS BOND : bond 0.00166 / 0.08 ( 3) SS BOND : angle 0.39956 / 0.23 ( 6) hydrogen bonds : bond 0.03172 / 2.21 ( 210) hydrogen bonds : angle 4.01738 / 2.98 ( 624) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.104 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 27 average time/residue: 0.0434 time to fit residues: 1.6952 Evaluate side-chains 32 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 56 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.0970 chunk 30 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 25 optimal weight: 0.3980 chunk 27 optimal weight: 0.0770 chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.156530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.111629 restraints weight = 3032.675| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.57 r_work: 0.3049 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.0759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3068 Z= 0.094 Angle : 0.413 5.274 4190 Z= 0.222 Chirality : 0.038 0.125 497 Planarity : 0.003 0.027 506 Dihedral : 3.633 14.903 433 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.00 % Allowed : 22.33 % Favored : 73.67 % 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: 1.60 (0.45), residues: 387 helix: 2.61 (0.35), residues: 224 sheet: -1.23 (0.66), residues: 58 loop : -1.03 (0.63), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 71 TYR 0.010 0.001 TYR A 219 PHE 0.005 0.001 PHE A 49 TRP 0.010 0.001 TRP A 313 HIS 0.004 0.001 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 ( 3065) covalent geometry : angle 0.41315 / 0.22 ( 4184) SS BOND : bond 0.00112 / 0.05 ( 3) SS BOND : angle 0.55742 / 0.32 ( 6) hydrogen bonds : bond 0.03081 / 2.16 ( 210) hydrogen bonds : angle 3.94404 / 2.93 ( 624) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 26 time to evaluate : 0.064 Fit side-chains REVERT: A 98 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7588 (ppp) REVERT: A 171 MET cc_start: 0.7429 (mmm) cc_final: 0.7140 (mmm) outliers start: 12 outliers final: 8 residues processed: 31 average time/residue: 0.0385 time to fit residues: 1.6187 Evaluate side-chains 34 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 56 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 31 optimal weight: 0.0170 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.155179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.110114 restraints weight = 3036.441| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.57 r_work: 0.3076 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.0777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3068 Z= 0.115 Angle : 0.426 5.366 4190 Z= 0.229 Chirality : 0.038 0.124 497 Planarity : 0.003 0.026 506 Dihedral : 3.653 15.858 433 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.67 % Allowed : 22.33 % Favored : 75.00 % 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: 1.54 (0.45), residues: 387 helix: 2.53 (0.34), residues: 224 sheet: -1.12 (0.66), residues: 58 loop : -1.05 (0.62), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 19 TYR 0.011 0.001 TYR A 219 PHE 0.006 0.001 PHE A 290 TRP 0.009 0.001 TRP A 313 HIS 0.004 0.001 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 3065) covalent geometry : angle 0.42599 / 0.23 ( 4184) SS BOND : bond 0.00129 / 0.06 ( 3) SS BOND : angle 0.48546 / 0.27 ( 6) hydrogen bonds : bond 0.03239 / 2.26 ( 210) hydrogen bonds : angle 3.93548 / 2.92 ( 624) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.103 Fit side-chains REVERT: A 98 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7498 (ppp) REVERT: A 171 MET cc_start: 0.7417 (mmm) cc_final: 0.7118 (mmm) outliers start: 8 outliers final: 6 residues processed: 30 average time/residue: 0.0387 time to fit residues: 1.6780 Evaluate side-chains 34 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 56 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 21 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.154316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.109019 restraints weight = 3042.385| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.58 r_work: 0.3070 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3068 Z= 0.124 Angle : 0.431 5.349 4190 Z= 0.232 Chirality : 0.038 0.121 497 Planarity : 0.003 0.027 506 Dihedral : 3.696 16.012 433 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.67 % Allowed : 23.00 % Favored : 74.33 % 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: 1.53 (0.44), residues: 387 helix: 2.48 (0.34), residues: 224 sheet: -0.98 (0.67), residues: 58 loop : -1.06 (0.62), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 19 TYR 0.011 0.001 TYR A 219 PHE 0.006 0.001 PHE A 290 TRP 0.009 0.001 TRP A 313 HIS 0.004 0.001 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 ( 3065) covalent geometry : angle 0.43125 / 0.23 ( 4184) SS BOND : bond 0.00116 / 0.05 ( 3) SS BOND : angle 0.43566 / 0.24 ( 6) hydrogen bonds : bond 0.03286 / 2.29 ( 210) hydrogen bonds : angle 3.95969 / 2.94 ( 624) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.106 Fit side-chains REVERT: A 98 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7536 (ppp) REVERT: A 171 MET cc_start: 0.7466 (mmm) cc_final: 0.7160 (mmm) outliers start: 8 outliers final: 6 residues processed: 32 average time/residue: 0.0298 time to fit residues: 1.3544 Evaluate side-chains 34 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 56 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 4 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 37 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 23 optimal weight: 0.5980 chunk 33 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.155649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.110551 restraints weight = 3072.273| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.58 r_work: 0.3146 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 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 : 0.002 0.024 3068 Z= 0.101 Angle : 0.417 5.275 4190 Z= 0.223 Chirality : 0.038 0.121 497 Planarity : 0.003 0.026 506 Dihedral : 3.626 15.323 433 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.33 % Allowed : 22.00 % Favored : 74.67 % 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: 1.69 (0.44), residues: 387 helix: 2.55 (0.34), residues: 224 sheet: -0.72 (0.66), residues: 60 loop : -0.98 (0.63), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 19 TYR 0.010 0.001 TYR A 219 PHE 0.006 0.001 PHE A 290 TRP 0.010 0.001 TRP A 313 HIS 0.004 0.001 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 ( 3065) covalent geometry : angle 0.41734 / 0.22 ( 4184) SS BOND : bond 0.00097 / 0.04 ( 3) SS BOND : angle 0.38641 / 0.21 ( 6) hydrogen bonds : bond 0.03150 / 2.20 ( 210) hydrogen bonds : angle 3.89871 / 2.90 ( 624) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.104 Fit side-chains REVERT: A 98 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8094 (ppp) REVERT: A 171 MET cc_start: 0.8058 (mmm) cc_final: 0.7744 (mmm) outliers start: 10 outliers final: 8 residues processed: 33 average time/residue: 0.0450 time to fit residues: 2.1103 Evaluate side-chains 36 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 56 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 17 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.154426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.109280 restraints weight = 3090.313| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.58 r_work: 0.2911 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.0905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3068 Z= 0.118 Angle : 0.428 5.336 4190 Z= 0.229 Chirality : 0.038 0.121 497 Planarity : 0.003 0.026 506 Dihedral : 3.654 15.914 433 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.00 % Allowed : 22.33 % Favored : 74.67 % 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: 1.61 (0.45), residues: 387 helix: 2.47 (0.34), residues: 224 sheet: -0.81 (0.66), residues: 62 loop : -0.93 (0.64), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 19 TYR 0.011 0.001 TYR A 219 PHE 0.006 0.001 PHE A 290 TRP 0.009 0.001 TRP A 313 HIS 0.004 0.001 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 3065) covalent geometry : angle 0.42780 / 0.23 ( 4184) SS BOND : bond 0.00102 / 0.05 ( 3) SS BOND : angle 0.52795 / 0.28 ( 6) hydrogen bonds : bond 0.03264 / 2.28 ( 210) hydrogen bonds : angle 3.92373 / 2.92 ( 624) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.108 Fit side-chains REVERT: A 98 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7301 (ppp) REVERT: A 171 MET cc_start: 0.7207 (mmm) cc_final: 0.6923 (mmm) outliers start: 9 outliers final: 8 residues processed: 32 average time/residue: 0.0468 time to fit residues: 2.0667 Evaluate side-chains 37 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 56 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 0.0980 chunk 3 optimal weight: 0.0970 chunk 31 optimal weight: 0.0170 chunk 24 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 0.0570 chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.1734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.158921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.113618 restraints weight = 3104.928| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.69 r_work: 0.3117 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3068 Z= 0.081 Angle : 0.402 5.155 4190 Z= 0.212 Chirality : 0.037 0.118 497 Planarity : 0.002 0.025 506 Dihedral : 3.494 14.515 433 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.33 % Allowed : 23.00 % Favored : 74.67 % 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: 1.83 (0.45), residues: 387 helix: 2.69 (0.34), residues: 224 sheet: -0.78 (0.66), residues: 62 loop : -0.89 (0.64), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 19 TYR 0.009 0.001 TYR A 219 PHE 0.006 0.001 PHE A 71 TRP 0.012 0.001 TRP A 313 HIS 0.003 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00161 / 0.08 ( 3065) covalent geometry : angle 0.40175 / 0.21 ( 4184) SS BOND : bond 0.00106 / 0.04 ( 3) SS BOND : angle 0.35650 / 0.20 ( 6) hydrogen bonds : bond 0.02870 / 2.01 ( 210) hydrogen bonds : angle 3.78123 / 2.81 ( 624) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.117 Fit side-chains REVERT: A 98 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7456 (ppp) REVERT: A 171 MET cc_start: 0.7355 (mmm) cc_final: 0.7065 (mmm) outliers start: 7 outliers final: 6 residues processed: 30 average time/residue: 0.0476 time to fit residues: 1.9544 Evaluate side-chains 33 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 56 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 23 optimal weight: 0.0000 chunk 17 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.157595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.114691 restraints weight = 3077.057| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.28 r_work: 0.3069 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3068 Z= 0.095 Angle : 0.409 5.222 4190 Z= 0.217 Chirality : 0.037 0.118 497 Planarity : 0.002 0.025 506 Dihedral : 3.497 14.402 433 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.00 % Allowed : 22.33 % Favored : 75.67 % 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: 1.71 (0.45), residues: 387 helix: 2.50 (0.34), residues: 230 sheet: -0.75 (0.72), residues: 55 loop : -1.02 (0.61), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 19 TYR 0.009 0.001 TYR A 219 PHE 0.005 0.001 PHE A 290 TRP 0.009 0.001 TRP A 313 HIS 0.003 0.001 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 ( 3065) covalent geometry : angle 0.40914 / 0.22 ( 4184) SS BOND : bond 0.00084 / 0.04 ( 3) SS BOND : angle 0.42190 / 0.23 ( 6) hydrogen bonds : bond 0.02993 / 2.10 ( 210) hydrogen bonds : angle 3.76197 / 2.80 ( 624) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.106 Fit side-chains REVERT: A 98 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7764 (ppp) REVERT: A 171 MET cc_start: 0.7706 (mmm) cc_final: 0.7416 (mmm) outliers start: 6 outliers final: 5 residues processed: 29 average time/residue: 0.0419 time to fit residues: 1.7415 Evaluate side-chains 32 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain B residue 56 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 28 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 31 optimal weight: 0.0570 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.6502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.155471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.112354 restraints weight = 3063.658| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.28 r_work: 0.3093 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3068 Z= 0.111 Angle : 0.423 5.293 4190 Z= 0.225 Chirality : 0.038 0.119 497 Planarity : 0.002 0.025 506 Dihedral : 3.577 15.185 433 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.33 % Allowed : 22.00 % Favored : 75.67 % 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: 1.64 (0.44), residues: 387 helix: 2.44 (0.34), residues: 230 sheet: -0.73 (0.72), residues: 55 loop : -1.04 (0.61), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 19 TYR 0.011 0.001 TYR A 219 PHE 0.007 0.001 PHE A 290 TRP 0.008 0.001 TRP A 313 HIS 0.004 0.001 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 3065) covalent geometry : angle 0.42326 / 0.23 ( 4184) SS BOND : bond 0.00093 / 0.04 ( 3) SS BOND : angle 0.47942 / 0.26 ( 6) hydrogen bonds : bond 0.03175 / 2.22 ( 210) hydrogen bonds : angle 3.80771 / 2.83 ( 624) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 908.86 seconds wall clock time: 16 minutes 14.26 seconds (974.26 seconds total)