Starting phenix.real_space_refine on Wed Jul 23 07:29:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggx_40024/07_2025/8ggx_40024.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggx_40024/07_2025/8ggx_40024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ggx_40024/07_2025/8ggx_40024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggx_40024/07_2025/8ggx_40024.map" model { file = "/net/cci-nas-00/data/ceres_data/8ggx_40024/07_2025/8ggx_40024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggx_40024/07_2025/8ggx_40024.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 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 13 5.16 5 C 1402 2.51 5 N 332 2.21 5 O 360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 2107 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2092 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ASP:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 79 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.27, per 1000 atoms: 1.08 Number of scatterers: 2107 At special positions: 0 Unit cell: (55.5328, 84.1669, 63.3421, 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 13 16.00 O 360 8.00 N 332 7.00 C 1402 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: 0.54 Conformation dependent library (CDL) restraints added in 259.3 milliseconds 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 538 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 0 sheets defined 87.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'R' and resid 32 through 61 removed outlier: 3.756A pdb=" N MET R 36 " --> pdb=" O TRP R 32 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 65 Processing helix chain 'R' and resid 68 through 96 removed outlier: 4.181A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix removed outlier: 4.182A pdb=" N ALA R 92 " --> pdb=" O PRO R 88 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N HIS R 93 " --> pdb=" O PHE R 89 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE R 94 " --> pdb=" O GLY R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 137 removed outlier: 4.008A pdb=" N CYS R 106 " --> pdb=" O GLY R 102 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLU R 107 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 164 removed outlier: 3.814A pdb=" N ALA R 150 " --> pdb=" O THR R 146 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 171 removed outlier: 3.617A pdb=" N ILE R 169 " --> pdb=" O SER R 165 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 187 Processing helix chain 'R' and resid 198 through 208 Processing helix chain 'R' and resid 208 through 237 removed outlier: 3.778A pdb=" N ASP R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS R 235 " --> pdb=" O GLN R 231 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 299 removed outlier: 4.490A pdb=" N LEU R 275 " --> pdb=" O ALA R 271 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.052A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.610A pdb=" N TYR R 308 " --> pdb=" O ARG R 304 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 322 removed outlier: 3.696A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 317 through 322' Processing helix chain 'R' and resid 322 through 327 removed outlier: 3.515A pdb=" N CYS R 327 " --> pdb=" O PRO R 323 " (cutoff:3.500A) Processing helix chain 'R' and resid 329 through 340 150 hydrogen bonds defined for protein. 447 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: 0.50 Time building geometry restraints manager: 0.65 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: 638 1.34 - 1.46: 542 1.46 - 1.58: 965 1.58 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 2163 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.451 -0.054 2.00e-02 2.50e+03 7.25e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.573 -0.050 2.00e-02 2.50e+03 6.13e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.441 -0.047 2.00e-02 2.50e+03 5.63e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.565 -0.045 2.00e-02 2.50e+03 5.13e+00 bond pdb=" CAI G1I R 501 " pdb=" NAN G1I R 501 " ideal model delta sigma weight residual 1.451 1.487 -0.036 2.00e-02 2.50e+03 3.22e+00 ... (remaining 2158 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 2833 1.11 - 2.23: 107 2.23 - 3.34: 16 3.34 - 4.46: 9 4.46 - 5.57: 4 Bond angle restraints: 2969 Sorted by residual: angle pdb=" C VAL R 295 " pdb=" N HIS R 296 " pdb=" CA HIS R 296 " ideal model delta sigma weight residual 120.31 116.98 3.33 1.52e+00 4.33e-01 4.80e+00 angle pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 112.63 118.20 -5.57 3.00e+00 1.11e-01 3.45e+00 angle pdb=" CA VAL R 295 " pdb=" C VAL R 295 " pdb=" N HIS R 296 " ideal model delta sigma weight residual 117.28 119.25 -1.97 1.16e+00 7.43e-01 2.89e+00 angle pdb=" N HIS R 296 " pdb=" CA HIS R 296 " pdb=" CB HIS R 296 " ideal model delta sigma weight residual 110.28 112.78 -2.50 1.55e+00 4.16e-01 2.60e+00 angle pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " pdb=" CAI G1I R 501 " ideal model delta sigma weight residual 110.89 115.65 -4.76 3.00e+00 1.11e-01 2.51e+00 ... (remaining 2964 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 1113 17.53 - 35.05: 92 35.05 - 52.58: 19 52.58 - 70.11: 2 70.11 - 87.63: 2 Dihedral angle restraints: 1228 sinusoidal: 400 harmonic: 828 Sorted by residual: dihedral pdb=" CA GLN R 299 " pdb=" C GLN R 299 " pdb=" N ASP R 300 " pdb=" CA ASP R 300 " ideal model delta harmonic sigma weight residual -180.00 -162.88 -17.12 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA GLN R 197 " pdb=" C GLN R 197 " pdb=" N ALA R 198 " pdb=" CA ALA R 198 " ideal model delta harmonic sigma weight residual 180.00 163.04 16.96 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CB GLU R 180 " pdb=" CG GLU R 180 " pdb=" CD GLU R 180 " pdb=" OE1 GLU R 180 " ideal model delta sinusoidal sigma weight residual 0.00 -87.63 87.63 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 1225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 230 0.034 - 0.067: 101 0.067 - 0.101: 25 0.101 - 0.135: 3 0.135 - 0.168: 1 Chirality restraints: 360 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.57 -0.17 2.00e-01 2.50e+01 7.07e-01 chirality pdb=" CA TYR R 326 " pdb=" N TYR R 326 " pdb=" C TYR R 326 " pdb=" CB TYR R 326 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.99e-01 chirality pdb=" CA LEU R 287 " pdb=" N LEU R 287 " pdb=" C LEU R 287 " pdb=" CB LEU R 287 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.11 2.00e-01 2.50e+01 2.76e-01 ... (remaining 357 not shown) Planarity restraints: 362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 173 " -0.010 2.00e-02 2.50e+03 1.01e-02 2.56e+00 pdb=" CG TRP R 173 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP R 173 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP R 173 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 173 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 173 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 173 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 173 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 173 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP R 173 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 167 " -0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO R 168 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO R 168 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 168 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER R 137 " -0.018 5.00e-02 4.00e+02 2.70e-02 1.16e+00 pdb=" N PRO R 138 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO R 138 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO R 138 " -0.015 5.00e-02 4.00e+02 ... (remaining 359 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 1031 2.97 - 3.45: 2339 3.45 - 3.94: 3154 3.94 - 4.42: 3299 4.42 - 4.90: 5590 Nonbonded interactions: 15413 Sorted by model distance: nonbonded pdb=" OE1 GLU R 180 " pdb=" N ALA R 181 " model vdw 2.489 3.120 nonbonded pdb=" OD2 ASP R 113 " pdb=" OAM G1I R 501 " model vdw 2.507 3.040 nonbonded pdb=" OE2 GLU R 107 " pdb=" OH TYR R 174 " model vdw 2.558 3.040 nonbonded pdb=" O TRP R 158 " pdb=" OG SER R 161 " model vdw 2.629 3.040 nonbonded pdb=" N THR R 146 " pdb=" O THR R 146 " model vdw 2.646 2.496 ... (remaining 15408 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.540 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: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 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 0.054 2163 Z= 0.184 Angle : 0.544 5.572 2969 Z= 0.293 Chirality : 0.039 0.168 360 Planarity : 0.004 0.030 362 Dihedral : 14.257 87.632 690 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.51), residues: 277 helix: 2.53 (0.36), residues: 200 sheet: None (None), residues: 0 loop : -1.62 (0.66), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 173 HIS 0.003 0.001 HIS R 178 PHE 0.014 0.001 PHE R 336 TYR 0.006 0.001 TYR R 326 ARG 0.001 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.13608 ( 150) hydrogen bonds : angle 3.95298 ( 447) covalent geometry : bond 0.00360 ( 2163) covalent geometry : angle 0.54448 ( 2969) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.246 Fit side-chains REVERT: R 192 ASP cc_start: 0.7667 (p0) cc_final: 0.7135 (p0) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1045 time to fit residues: 6.4731 Evaluate side-chains 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.159912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.142719 restraints weight = 3499.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.145282 restraints weight = 2005.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.147157 restraints weight = 1341.545| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2163 Z= 0.173 Angle : 0.554 5.344 2969 Z= 0.312 Chirality : 0.040 0.130 360 Planarity : 0.004 0.032 362 Dihedral : 4.835 17.501 309 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.98 % Allowed : 8.96 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.52), residues: 277 helix: 2.29 (0.36), residues: 203 sheet: None (None), residues: 0 loop : -1.82 (0.71), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 173 HIS 0.005 0.001 HIS R 178 PHE 0.011 0.001 PHE R 104 TYR 0.018 0.002 TYR R 185 ARG 0.001 0.000 ARG R 131 Details of bonding type rmsd hydrogen bonds : bond 0.06245 ( 150) hydrogen bonds : angle 3.73706 ( 447) covalent geometry : bond 0.00387 ( 2163) covalent geometry : angle 0.55448 ( 2969) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.252 Fit side-chains REVERT: R 185 TYR cc_start: 0.8028 (m-80) cc_final: 0.7680 (m-80) outliers start: 10 outliers final: 7 residues processed: 48 average time/residue: 0.1009 time to fit residues: 6.0411 Evaluate side-chains 44 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 327 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 10 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 0.0370 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 23 optimal weight: 0.0670 chunk 14 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.163973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.147197 restraints weight = 3468.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.150021 restraints weight = 1922.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.151920 restraints weight = 1295.115| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2163 Z= 0.124 Angle : 0.494 5.319 2969 Z= 0.277 Chirality : 0.038 0.128 360 Planarity : 0.003 0.025 362 Dihedral : 4.692 16.599 309 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.98 % Allowed : 15.42 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.52), residues: 277 helix: 2.37 (0.36), residues: 204 sheet: None (None), residues: 0 loop : -1.88 (0.68), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 173 HIS 0.002 0.001 HIS R 178 PHE 0.014 0.001 PHE R 104 TYR 0.017 0.001 TYR R 185 ARG 0.000 0.000 ARG R 151 Details of bonding type rmsd hydrogen bonds : bond 0.05155 ( 150) hydrogen bonds : angle 3.50858 ( 447) covalent geometry : bond 0.00255 ( 2163) covalent geometry : angle 0.49357 ( 2969) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.226 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 44 average time/residue: 0.1026 time to fit residues: 5.6654 Evaluate side-chains 41 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 327 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 2 optimal weight: 0.0070 chunk 6 optimal weight: 0.0870 chunk 11 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.164051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.146745 restraints weight = 3343.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.149513 restraints weight = 1908.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.151381 restraints weight = 1268.322| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2163 Z= 0.125 Angle : 0.487 5.301 2969 Z= 0.273 Chirality : 0.037 0.125 360 Planarity : 0.003 0.026 362 Dihedral : 4.499 16.452 309 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.99 % Allowed : 14.43 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.51), residues: 277 helix: 2.37 (0.36), residues: 205 sheet: None (None), residues: 0 loop : -2.00 (0.65), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 173 HIS 0.002 0.001 HIS R 178 PHE 0.007 0.001 PHE R 193 TYR 0.011 0.001 TYR R 326 ARG 0.000 0.000 ARG R 131 Details of bonding type rmsd hydrogen bonds : bond 0.05031 ( 150) hydrogen bonds : angle 3.52075 ( 447) covalent geometry : bond 0.00264 ( 2163) covalent geometry : angle 0.48685 ( 2969) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.197 Fit side-chains REVERT: R 180 GLU cc_start: 0.7619 (tp30) cc_final: 0.7322 (tp30) outliers start: 6 outliers final: 5 residues processed: 43 average time/residue: 0.0982 time to fit residues: 5.3213 Evaluate side-chains 43 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 327 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 0.0570 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.162149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.144757 restraints weight = 3485.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.147432 restraints weight = 1976.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.149396 restraints weight = 1320.533| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2163 Z= 0.130 Angle : 0.490 5.309 2969 Z= 0.273 Chirality : 0.038 0.125 360 Planarity : 0.003 0.026 362 Dihedral : 4.512 16.277 309 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.98 % Allowed : 16.42 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.51), residues: 277 helix: 2.40 (0.36), residues: 204 sheet: None (None), residues: 0 loop : -2.18 (0.63), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 173 HIS 0.002 0.001 HIS R 296 PHE 0.008 0.001 PHE R 194 TYR 0.011 0.001 TYR R 326 ARG 0.000 0.000 ARG R 131 Details of bonding type rmsd hydrogen bonds : bond 0.05237 ( 150) hydrogen bonds : angle 3.59626 ( 447) covalent geometry : bond 0.00278 ( 2163) covalent geometry : angle 0.48951 ( 2969) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.225 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 43 average time/residue: 0.1025 time to fit residues: 5.5322 Evaluate side-chains 41 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 327 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 2 optimal weight: 0.0060 chunk 26 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.1980 chunk 23 optimal weight: 0.7980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.161835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.144448 restraints weight = 3441.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.147133 restraints weight = 1973.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.149078 restraints weight = 1311.806| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2163 Z= 0.123 Angle : 0.478 5.311 2969 Z= 0.267 Chirality : 0.037 0.124 360 Planarity : 0.003 0.025 362 Dihedral : 4.423 16.234 309 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.98 % Allowed : 17.41 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.52), residues: 277 helix: 2.41 (0.36), residues: 205 sheet: None (None), residues: 0 loop : -2.21 (0.63), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 173 HIS 0.002 0.001 HIS R 296 PHE 0.008 0.001 PHE R 193 TYR 0.010 0.001 TYR R 326 ARG 0.000 0.000 ARG R 151 Details of bonding type rmsd hydrogen bonds : bond 0.05011 ( 150) hydrogen bonds : angle 3.56513 ( 447) covalent geometry : bond 0.00258 ( 2163) covalent geometry : angle 0.47762 ( 2969) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.186 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 42 average time/residue: 0.1010 time to fit residues: 5.3464 Evaluate side-chains 41 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 15 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.160135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.142557 restraints weight = 3501.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.145155 restraints weight = 2015.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.147044 restraints weight = 1354.597| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2163 Z= 0.152 Angle : 0.515 5.316 2969 Z= 0.288 Chirality : 0.038 0.124 360 Planarity : 0.003 0.028 362 Dihedral : 4.528 16.189 309 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.98 % Allowed : 20.40 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.51), residues: 277 helix: 2.28 (0.36), residues: 204 sheet: None (None), residues: 0 loop : -2.24 (0.64), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 173 HIS 0.002 0.001 HIS R 296 PHE 0.008 0.001 PHE R 193 TYR 0.012 0.002 TYR R 326 ARG 0.001 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.05808 ( 150) hydrogen bonds : angle 3.71034 ( 447) covalent geometry : bond 0.00335 ( 2163) covalent geometry : angle 0.51461 ( 2969) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.319 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 42 average time/residue: 0.1246 time to fit residues: 6.7725 Evaluate side-chains 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.160914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.143786 restraints weight = 3585.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.146435 restraints weight = 2038.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.148418 restraints weight = 1355.873| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2163 Z= 0.142 Angle : 0.504 5.334 2969 Z= 0.283 Chirality : 0.038 0.127 360 Planarity : 0.003 0.027 362 Dihedral : 4.518 16.340 309 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.49 % Allowed : 22.89 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.51), residues: 277 helix: 2.18 (0.36), residues: 210 sheet: None (None), residues: 0 loop : -2.21 (0.66), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 173 HIS 0.002 0.001 HIS R 296 PHE 0.007 0.001 PHE R 289 TYR 0.012 0.001 TYR R 326 ARG 0.000 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.05616 ( 150) hydrogen bonds : angle 3.68987 ( 447) covalent geometry : bond 0.00309 ( 2163) covalent geometry : angle 0.50395 ( 2969) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.244 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 39 average time/residue: 0.1112 time to fit residues: 5.4696 Evaluate side-chains 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.162166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.145201 restraints weight = 3509.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.147822 restraints weight = 2008.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.149710 restraints weight = 1354.144| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2163 Z= 0.142 Angle : 0.511 5.324 2969 Z= 0.283 Chirality : 0.038 0.126 360 Planarity : 0.003 0.029 362 Dihedral : 4.503 16.263 309 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.48 % Allowed : 23.38 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.51), residues: 277 helix: 2.14 (0.36), residues: 211 sheet: None (None), residues: 0 loop : -2.43 (0.65), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 173 HIS 0.002 0.001 HIS R 296 PHE 0.007 0.001 PHE R 289 TYR 0.012 0.001 TYR R 326 ARG 0.000 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.05615 ( 150) hydrogen bonds : angle 3.68175 ( 447) covalent geometry : bond 0.00307 ( 2163) covalent geometry : angle 0.51111 ( 2969) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.222 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 40 average time/residue: 0.1011 time to fit residues: 5.2316 Evaluate side-chains 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.160215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.143179 restraints weight = 3569.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.145752 restraints weight = 2061.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.147631 restraints weight = 1394.116| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2163 Z= 0.152 Angle : 0.524 5.325 2969 Z= 0.291 Chirality : 0.038 0.126 360 Planarity : 0.003 0.030 362 Dihedral : 4.548 16.395 309 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.99 % Allowed : 23.88 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.51), residues: 277 helix: 2.09 (0.36), residues: 211 sheet: None (None), residues: 0 loop : -2.43 (0.66), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 173 HIS 0.002 0.001 HIS R 296 PHE 0.007 0.001 PHE R 289 TYR 0.012 0.002 TYR R 326 ARG 0.000 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.05838 ( 150) hydrogen bonds : angle 3.69827 ( 447) covalent geometry : bond 0.00335 ( 2163) covalent geometry : angle 0.52387 ( 2969) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.190 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 40 average time/residue: 0.1028 time to fit residues: 5.1504 Evaluate side-chains 41 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 0.0670 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.161094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.143954 restraints weight = 3477.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.146612 restraints weight = 1987.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.148561 restraints weight = 1331.553| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2163 Z= 0.133 Angle : 0.504 5.312 2969 Z= 0.279 Chirality : 0.038 0.126 360 Planarity : 0.003 0.029 362 Dihedral : 4.455 16.319 309 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.99 % Allowed : 23.88 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.52), residues: 277 helix: 2.20 (0.36), residues: 210 sheet: None (None), residues: 0 loop : -2.22 (0.67), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 173 HIS 0.002 0.001 HIS R 296 PHE 0.010 0.001 PHE R 289 TYR 0.011 0.001 TYR R 326 ARG 0.000 0.000 ARG R 131 Details of bonding type rmsd hydrogen bonds : bond 0.05390 ( 150) hydrogen bonds : angle 3.61665 ( 447) covalent geometry : bond 0.00282 ( 2163) covalent geometry : angle 0.50426 ( 2969) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1269.78 seconds wall clock time: 23 minutes 1.69 seconds (1381.69 seconds total)