Starting phenix.real_space_refine on Wed Jul 23 06:46:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7us9_26729/07_2025/7us9_26729.cif Found real_map, /net/cci-nas-00/data/ceres_data/7us9_26729/07_2025/7us9_26729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7us9_26729/07_2025/7us9_26729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7us9_26729/07_2025/7us9_26729.map" model { file = "/net/cci-nas-00/data/ceres_data/7us9_26729/07_2025/7us9_26729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7us9_26729/07_2025/7us9_26729.cif" } resolution = 3.8 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 4 5.16 5 C 744 2.51 5 N 185 2.21 5 O 194 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 1127 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1071 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 137} Chain breaks: 7 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.56, per 1000 atoms: 3.16 Number of scatterers: 1127 At special positions: 0 Unit cell: (50.58, 48.894, 59.853, 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 4 16.00 O 194 8.00 N 185 7.00 C 744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 153 " distance=2.09 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A 301 " - " ASN A 42 " " NAG A 302 " - " ASN A 242 " " NAG B 1 " - " ASN A 249 " Time building additional restraints: 0.33 Conformation dependent library (CDL) restraints added in 130.8 milliseconds 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 274 Finding SS restraints... Secondary structure from input PDB file: 1 helices and 3 sheets defined 9.7% alpha, 43.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 32 through 45 removed outlier: 4.150A pdb=" N ILE A 36 " --> pdb=" O HIS A 32 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 57 Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 81 removed outlier: 7.641A pdb=" N PHE A 202 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LYS A 110 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N THR A 204 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 109 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TYR A 112 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE A 130 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN A 156 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE A 132 " --> pdb=" O ARG A 154 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 191 through 196 removed outlier: 3.514A pdb=" N ALA A 85 " --> pdb=" O VAL A 230 " (cutoff:3.500A) 54 hydrogen bonds defined for protein. 141 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: 0.28 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: 1.20 - 1.33: 251 1.33 - 1.46: 358 1.46 - 1.58: 546 1.58 - 1.71: 1 1.71 - 1.84: 6 Bond restraints: 1162 Sorted by residual: bond pdb=" N PRO A 111 " pdb=" CD PRO A 111 " ideal model delta sigma weight residual 1.474 1.381 0.093 1.40e-02 5.10e+03 4.37e+01 bond pdb=" CZ2 TRP A 225 " pdb=" CH2 TRP A 225 " ideal model delta sigma weight residual 1.368 1.455 -0.087 1.90e-02 2.77e+03 2.10e+01 bond pdb=" CD2 TRP A 225 " pdb=" CE3 TRP A 225 " ideal model delta sigma weight residual 1.398 1.468 -0.070 1.60e-02 3.91e+03 1.90e+01 bond pdb=" CB LEU A 76 " pdb=" CG LEU A 76 " ideal model delta sigma weight residual 1.530 1.615 -0.085 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C LEU A 47 " pdb=" N PRO A 48 " ideal model delta sigma weight residual 1.329 1.371 -0.042 1.18e-02 7.18e+03 1.24e+01 ... (remaining 1157 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 1429 2.34 - 4.69: 128 4.69 - 7.03: 27 7.03 - 9.38: 3 9.38 - 11.72: 2 Bond angle restraints: 1589 Sorted by residual: angle pdb=" N ILE A 195 " pdb=" CA ILE A 195 " pdb=" C ILE A 195 " ideal model delta sigma weight residual 108.11 117.48 -9.37 1.40e+00 5.10e-01 4.47e+01 angle pdb=" C PHE A 159 " pdb=" N PRO A 160 " pdb=" CA PRO A 160 " ideal model delta sigma weight residual 120.31 126.85 -6.54 9.80e-01 1.04e+00 4.45e+01 angle pdb=" C PRO A 48 " pdb=" N PRO A 49 " pdb=" CA PRO A 49 " ideal model delta sigma weight residual 119.84 127.79 -7.95 1.25e+00 6.40e-01 4.05e+01 angle pdb=" C LEU A 47 " pdb=" N PRO A 48 " pdb=" CA PRO A 48 " ideal model delta sigma weight residual 120.38 126.66 -6.28 1.03e+00 9.43e-01 3.72e+01 angle pdb=" N VAL A 78 " pdb=" CA VAL A 78 " pdb=" CB VAL A 78 " ideal model delta sigma weight residual 110.72 104.39 6.33 1.09e+00 8.42e-01 3.37e+01 ... (remaining 1584 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.01: 623 8.01 - 16.02: 44 16.02 - 24.03: 10 24.03 - 32.04: 7 32.04 - 40.05: 4 Dihedral angle restraints: 688 sinusoidal: 266 harmonic: 422 Sorted by residual: dihedral pdb=" C GLN A 63 " pdb=" N GLN A 63 " pdb=" CA GLN A 63 " pdb=" CB GLN A 63 " ideal model delta harmonic sigma weight residual -122.60 -130.32 7.72 0 2.50e+00 1.60e-01 9.54e+00 dihedral pdb=" CA ILE A 195 " pdb=" CB ILE A 195 " pdb=" CG1 ILE A 195 " pdb=" CD1 ILE A 195 " ideal model delta sinusoidal sigma weight residual 60.00 100.05 -40.05 3 1.50e+01 4.44e-03 7.12e+00 dihedral pdb=" C LYS A 110 " pdb=" N LYS A 110 " pdb=" CA LYS A 110 " pdb=" CB LYS A 110 " ideal model delta harmonic sigma weight residual -122.60 -116.09 -6.51 0 2.50e+00 1.60e-01 6.77e+00 ... (remaining 685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 122 0.078 - 0.157: 30 0.157 - 0.235: 13 0.235 - 0.313: 9 0.313 - 0.392: 4 Chirality restraints: 178 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.42e+01 chirality pdb=" C2 NAG B 1 " pdb=" C1 NAG B 1 " pdb=" C3 NAG B 1 " pdb=" N2 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.88 0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CG LEU A 76 " pdb=" CB LEU A 76 " pdb=" CD1 LEU A 76 " pdb=" CD2 LEU A 76 " both_signs ideal model delta sigma weight residual False -2.59 -2.97 0.38 2.00e-01 2.50e+01 3.59e+00 ... (remaining 175 not shown) Planarity restraints: 196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 42 " -0.046 2.00e-02 2.50e+03 4.80e-02 2.88e+01 pdb=" CG ASN A 42 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN A 42 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 42 " 0.075 2.00e-02 2.50e+03 pdb=" C1 NAG A 301 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 242 " -0.039 2.00e-02 2.50e+03 4.07e-02 2.07e+01 pdb=" CG ASN A 242 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN A 242 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 242 " 0.063 2.00e-02 2.50e+03 pdb=" C1 NAG A 302 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 64 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" C PRO A 64 " 0.029 2.00e-02 2.50e+03 pdb=" O PRO A 64 " -0.011 2.00e-02 2.50e+03 pdb=" N TRP A 65 " -0.010 2.00e-02 2.50e+03 ... (remaining 193 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 519 2.97 - 3.45: 846 3.45 - 3.94: 1656 3.94 - 4.42: 1735 4.42 - 4.90: 3029 Nonbonded interactions: 7785 Sorted by model distance: nonbonded pdb=" O LYS A 110 " pdb=" CD PRO A 111 " model vdw 2.489 2.752 nonbonded pdb=" O GLN A 178 " pdb=" CA TRP A 179 " model vdw 2.627 2.776 nonbonded pdb=" N GLY A 109 " pdb=" O GLY A 109 " model vdw 2.636 2.496 nonbonded pdb=" N MET A 80 " pdb=" O MET A 80 " model vdw 2.641 2.496 nonbonded pdb=" O HIS A 189 " pdb=" ND1 HIS A 189 " model vdw 2.643 3.120 ... (remaining 7780 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 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: 5.360 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: 0.010 Set scattering table: 0.020 Process input model: 11.120 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 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 : 0.015 0.093 1167 Z= 0.820 Angle : 1.599 11.720 1603 Z= 1.016 Chirality : 0.112 0.392 178 Planarity : 0.005 0.017 193 Dihedral : 7.489 40.047 411 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.07 (0.73), residues: 129 helix: 3.26 (1.42), residues: 12 sheet: 1.80 (0.75), residues: 47 loop : -0.57 (0.71), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP A 65 HIS 0.004 0.002 HIS A 189 PHE 0.011 0.003 PHE A 227 TYR 0.015 0.004 TYR A 43 ARG 0.002 0.000 ARG A 154 Details of bonding type rmsd link_NAG-ASN : bond 0.06837 ( 3) link_NAG-ASN : angle 2.22484 ( 9) link_BETA1-4 : bond 0.07242 ( 1) link_BETA1-4 : angle 4.52926 ( 3) hydrogen bonds : bond 0.18023 ( 54) hydrogen bonds : angle 7.59859 ( 141) SS BOND : bond 0.05691 ( 1) SS BOND : angle 2.69427 ( 2) covalent geometry : bond 0.01459 ( 1162) covalent geometry : angle 1.58180 ( 1589) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.119 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1192 time to fit residues: 4.4341 Evaluate side-chains 21 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 11 optimal weight: 0.0970 chunk 10 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 3 optimal weight: 0.0970 chunk 7 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 chunk 8 optimal weight: 0.1980 chunk 12 optimal weight: 0.2980 chunk 13 optimal weight: 0.0770 chunk 9 optimal weight: 0.6980 overall best weight: 0.1534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.172618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.152233 restraints weight = 1781.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.154981 restraints weight = 1177.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.156655 restraints weight = 867.543| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1167 Z= 0.150 Angle : 0.743 8.661 1603 Z= 0.367 Chirality : 0.053 0.217 178 Planarity : 0.005 0.029 193 Dihedral : 7.571 49.658 235 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.47 % Allowed : 11.11 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.39 (0.77), residues: 129 helix: 3.66 (1.28), residues: 12 sheet: 1.50 (0.60), residues: 73 loop : -0.95 (1.05), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 179 HIS 0.001 0.000 HIS A 189 PHE 0.010 0.002 PHE A 59 TYR 0.008 0.001 TYR A 43 ARG 0.000 0.000 ARG A 194 Details of bonding type rmsd link_NAG-ASN : bond 0.00835 ( 3) link_NAG-ASN : angle 4.30103 ( 9) link_BETA1-4 : bond 0.00035 ( 1) link_BETA1-4 : angle 1.81635 ( 3) hydrogen bonds : bond 0.04684 ( 54) hydrogen bonds : angle 5.89389 ( 141) SS BOND : bond 0.00205 ( 1) SS BOND : angle 1.45486 ( 2) covalent geometry : bond 0.00321 ( 1162) covalent geometry : angle 0.66596 ( 1589) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.105 Fit side-chains REVERT: A 199 ASN cc_start: 0.8206 (OUTLIER) cc_final: 0.7808 (t0) outliers start: 2 outliers final: 1 residues processed: 21 average time/residue: 0.0597 time to fit residues: 1.6317 Evaluate side-chains 16 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 199 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 4 optimal weight: 0.4980 chunk 9 optimal weight: 0.0870 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 1 optimal weight: 0.0170 chunk 5 optimal weight: 0.4980 chunk 13 optimal weight: 0.1980 chunk 12 optimal weight: 0.4980 chunk 0 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 overall best weight: 0.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.171730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.150845 restraints weight = 1760.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.152841 restraints weight = 1326.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.154118 restraints weight = 1080.520| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 1167 Z= 0.189 Angle : 0.828 10.352 1603 Z= 0.408 Chirality : 0.052 0.166 178 Planarity : 0.007 0.062 193 Dihedral : 7.050 36.814 235 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.70 % Allowed : 9.88 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.49 (0.73), residues: 129 helix: 2.49 (1.34), residues: 12 sheet: 0.95 (0.60), residues: 75 loop : -1.55 (0.89), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 179 HIS 0.002 0.001 HIS A 189 PHE 0.020 0.002 PHE A 197 TYR 0.009 0.001 TYR A 43 ARG 0.001 0.000 ARG A 194 Details of bonding type rmsd link_NAG-ASN : bond 0.01329 ( 3) link_NAG-ASN : angle 4.16868 ( 9) link_BETA1-4 : bond 0.00015 ( 1) link_BETA1-4 : angle 2.05385 ( 3) hydrogen bonds : bond 0.04407 ( 54) hydrogen bonds : angle 5.33872 ( 141) SS BOND : bond 0.00334 ( 1) SS BOND : angle 1.10751 ( 2) covalent geometry : bond 0.00412 ( 1162) covalent geometry : angle 0.76437 ( 1589) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 16 time to evaluate : 0.118 Fit side-chains REVERT: A 80 MET cc_start: 0.7458 (mmm) cc_final: 0.7064 (mmm) outliers start: 3 outliers final: 3 residues processed: 18 average time/residue: 0.0649 time to fit residues: 1.5240 Evaluate side-chains 17 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 199 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 4 optimal weight: 0.3980 chunk 10 optimal weight: 0.5980 chunk 3 optimal weight: 0.3980 chunk 1 optimal weight: 0.3980 chunk 12 optimal weight: 0.5980 chunk 9 optimal weight: 0.0770 chunk 13 optimal weight: 0.3980 chunk 2 optimal weight: 0.2980 chunk 0 optimal weight: 0.3980 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 overall best weight: 0.3138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.165860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.146532 restraints weight = 1767.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.148637 restraints weight = 1226.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.149716 restraints weight = 951.876| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 1167 Z= 0.199 Angle : 0.760 10.794 1603 Z= 0.368 Chirality : 0.055 0.272 178 Planarity : 0.006 0.048 193 Dihedral : 7.069 39.411 235 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.47 % Allowed : 11.11 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.28 (0.72), residues: 129 helix: 2.22 (1.33), residues: 12 sheet: 0.73 (0.59), residues: 77 loop : -1.54 (0.88), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 179 HIS 0.001 0.001 HIS A 189 PHE 0.010 0.002 PHE A 59 TYR 0.010 0.001 TYR A 235 ARG 0.001 0.000 ARG A 194 Details of bonding type rmsd link_NAG-ASN : bond 0.01086 ( 3) link_NAG-ASN : angle 4.83040 ( 9) link_BETA1-4 : bond 0.00107 ( 1) link_BETA1-4 : angle 2.25491 ( 3) hydrogen bonds : bond 0.04327 ( 54) hydrogen bonds : angle 5.12745 ( 141) SS BOND : bond 0.00316 ( 1) SS BOND : angle 0.88049 ( 2) covalent geometry : bond 0.00452 ( 1162) covalent geometry : angle 0.66284 ( 1589) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.110 Fit side-chains REVERT: A 36 ILE cc_start: 0.9049 (mm) cc_final: 0.8837 (mt) REVERT: A 80 MET cc_start: 0.7599 (mmm) cc_final: 0.7201 (mmm) outliers start: 2 outliers final: 1 residues processed: 18 average time/residue: 0.0614 time to fit residues: 1.4666 Evaluate side-chains 14 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 0.1980 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 chunk 0 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 13 optimal weight: 0.0570 chunk 4 optimal weight: 0.2980 chunk 1 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 overall best weight: 0.3298 ------------------------------------------------------------------------------- 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 = 0.3888 r_free = 0.3888 target = 0.166508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.144351 restraints weight = 1741.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.146822 restraints weight = 1184.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.148610 restraints weight = 916.782| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 1167 Z= 0.210 Angle : 0.834 10.666 1603 Z= 0.419 Chirality : 0.055 0.206 178 Planarity : 0.006 0.042 193 Dihedral : 7.331 39.112 235 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.23 % Allowed : 19.75 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -0.13 (0.72), residues: 129 helix: 2.36 (1.44), residues: 12 sheet: 0.57 (0.60), residues: 77 loop : -2.21 (0.77), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 179 HIS 0.002 0.001 HIS A 157 PHE 0.028 0.003 PHE A 39 TYR 0.011 0.001 TYR A 43 ARG 0.001 0.000 ARG A 194 Details of bonding type rmsd link_NAG-ASN : bond 0.00809 ( 3) link_NAG-ASN : angle 4.22742 ( 9) link_BETA1-4 : bond 0.00281 ( 1) link_BETA1-4 : angle 2.41053 ( 3) hydrogen bonds : bond 0.04310 ( 54) hydrogen bonds : angle 5.08872 ( 141) SS BOND : bond 0.00375 ( 1) SS BOND : angle 0.91177 ( 2) covalent geometry : bond 0.00478 ( 1162) covalent geometry : angle 0.76754 ( 1589) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.121 Fit side-chains REVERT: A 36 ILE cc_start: 0.9146 (mm) cc_final: 0.8915 (mt) REVERT: A 193 TYR cc_start: 0.7690 (m-80) cc_final: 0.7470 (m-80) outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.1070 time to fit residues: 2.0890 Evaluate side-chains 14 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 10 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 8 optimal weight: 0.1980 chunk 9 optimal weight: 0.1980 chunk 7 optimal weight: 0.5980 chunk 6 optimal weight: 0.1980 chunk 3 optimal weight: 0.1980 chunk 0 optimal weight: 0.6980 chunk 4 optimal weight: 0.2980 chunk 5 optimal weight: 0.8980 chunk 1 optimal weight: 0.2980 overall best weight: 0.2180 ------------------------------------------------------------------------------- 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 = 0.3912 r_free = 0.3912 target = 0.168792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.147714 restraints weight = 1763.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.150116 restraints weight = 1234.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.151830 restraints weight = 964.591| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 1167 Z= 0.174 Angle : 0.924 17.694 1603 Z= 0.427 Chirality : 0.063 0.502 178 Planarity : 0.005 0.040 193 Dihedral : 8.877 38.302 235 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.47 % Allowed : 20.99 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.77 % 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: -0.15 (0.72), residues: 129 helix: 3.14 (1.39), residues: 12 sheet: 0.50 (0.62), residues: 73 loop : -2.11 (0.71), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 179 HIS 0.001 0.000 HIS A 157 PHE 0.009 0.001 PHE A 202 TYR 0.008 0.001 TYR A 43 ARG 0.001 0.000 ARG A 194 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 3) link_NAG-ASN : angle 6.69186 ( 9) link_BETA1-4 : bond 0.00025 ( 1) link_BETA1-4 : angle 2.36514 ( 3) hydrogen bonds : bond 0.03722 ( 54) hydrogen bonds : angle 4.89448 ( 141) SS BOND : bond 0.00261 ( 1) SS BOND : angle 0.80351 ( 2) covalent geometry : bond 0.00387 ( 1162) covalent geometry : angle 0.77196 ( 1589) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.109 Fit side-chains REVERT: A 36 ILE cc_start: 0.9103 (mm) cc_final: 0.8799 (mt) REVERT: A 193 TYR cc_start: 0.7667 (m-80) cc_final: 0.7375 (m-80) outliers start: 2 outliers final: 1 residues processed: 18 average time/residue: 0.1001 time to fit residues: 2.1640 Evaluate side-chains 16 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 5 optimal weight: 0.0770 chunk 1 optimal weight: 0.3980 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 0 optimal weight: 0.5980 chunk 13 optimal weight: 0.0050 chunk 4 optimal weight: 0.4980 chunk 11 optimal weight: 0.3980 chunk 2 optimal weight: 0.4980 chunk 10 optimal weight: 0.0970 chunk 6 optimal weight: 0.6980 overall best weight: 0.1950 ------------------------------------------------------------------------------- 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 = 0.3914 r_free = 0.3914 target = 0.169486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.148002 restraints weight = 1706.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.150461 restraints weight = 1212.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.152030 restraints weight = 953.144| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 1167 Z= 0.144 Angle : 0.785 9.377 1603 Z= 0.385 Chirality : 0.068 0.594 178 Planarity : 0.006 0.038 193 Dihedral : 8.556 56.438 235 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.23 % Allowed : 20.99 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.77 % 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: -0.11 (0.73), residues: 129 helix: 4.01 (1.32), residues: 12 sheet: 0.48 (0.63), residues: 74 loop : -2.33 (0.68), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 179 HIS 0.001 0.000 HIS A 157 PHE 0.017 0.002 PHE A 197 TYR 0.007 0.001 TYR A 43 ARG 0.001 0.000 ARG A 194 Details of bonding type rmsd link_NAG-ASN : bond 0.00415 ( 3) link_NAG-ASN : angle 4.59556 ( 9) link_BETA1-4 : bond 0.00255 ( 1) link_BETA1-4 : angle 2.38633 ( 3) hydrogen bonds : bond 0.03447 ( 54) hydrogen bonds : angle 4.70265 ( 141) SS BOND : bond 0.00248 ( 1) SS BOND : angle 0.80225 ( 2) covalent geometry : bond 0.00331 ( 1162) covalent geometry : angle 0.70084 ( 1589) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.132 Fit side-chains REVERT: A 36 ILE cc_start: 0.9020 (mm) cc_final: 0.8744 (mt) REVERT: A 39 PHE cc_start: 0.9269 (t80) cc_final: 0.8851 (t80) REVERT: A 193 TYR cc_start: 0.7666 (m-80) cc_final: 0.7383 (m-80) outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 0.1426 time to fit residues: 2.9011 Evaluate side-chains 17 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 2 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 0 optimal weight: 0.0670 chunk 5 optimal weight: 0.0270 chunk 8 optimal weight: 0.6980 chunk 3 optimal weight: 0.3980 chunk 11 optimal weight: 0.4980 chunk 1 optimal weight: 0.0070 chunk 9 optimal weight: 0.3980 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.1980 overall best weight: 0.1394 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.170975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.148379 restraints weight = 1764.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.151005 restraints weight = 1165.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.153017 restraints weight = 887.920| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 1167 Z= 0.123 Angle : 0.721 8.517 1603 Z= 0.340 Chirality : 0.076 0.770 178 Planarity : 0.005 0.037 193 Dihedral : 7.490 36.283 235 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.23 % Allowed : 22.22 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.77 % 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: 0.02 (0.73), residues: 129 helix: 4.45 (1.30), residues: 12 sheet: 0.54 (0.63), residues: 74 loop : -2.33 (0.66), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 65 HIS 0.001 0.000 HIS A 157 PHE 0.007 0.001 PHE A 202 TYR 0.006 0.001 TYR A 43 ARG 0.000 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 3) link_NAG-ASN : angle 3.67483 ( 9) link_BETA1-4 : bond 0.00081 ( 1) link_BETA1-4 : angle 2.38801 ( 3) hydrogen bonds : bond 0.03154 ( 54) hydrogen bonds : angle 4.59457 ( 141) SS BOND : bond 0.00191 ( 1) SS BOND : angle 0.69942 ( 2) covalent geometry : bond 0.00280 ( 1162) covalent geometry : angle 0.66104 ( 1589) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.117 Fit side-chains REVERT: A 36 ILE cc_start: 0.9029 (mm) cc_final: 0.8754 (mt) REVERT: A 193 TYR cc_start: 0.7585 (m-80) cc_final: 0.7290 (m-80) outliers start: 1 outliers final: 1 residues processed: 20 average time/residue: 0.1386 time to fit residues: 3.1529 Evaluate side-chains 17 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.0870 chunk 0 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 0.1980 chunk 6 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 8 optimal weight: 0.0980 chunk 11 optimal weight: 0.0980 chunk 1 optimal weight: 0.0980 overall best weight: 0.1158 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.164329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.142806 restraints weight = 1768.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.145642 restraints weight = 1140.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.147587 restraints weight = 841.577| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.5480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 1167 Z= 0.139 Angle : 0.931 17.620 1603 Z= 0.407 Chirality : 0.117 1.374 178 Planarity : 0.006 0.038 193 Dihedral : 7.519 35.188 235 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.23 % Allowed : 25.93 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.77 % 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: 0.20 (0.74), residues: 129 helix: 5.13 (1.30), residues: 12 sheet: 0.58 (0.63), residues: 74 loop : -2.25 (0.68), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 201 HIS 0.001 0.000 HIS A 157 PHE 0.040 0.002 PHE A 39 TYR 0.006 0.001 TYR A 43 ARG 0.000 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00330 ( 3) link_NAG-ASN : angle 7.12699 ( 9) link_BETA1-4 : bond 0.00099 ( 1) link_BETA1-4 : angle 2.32919 ( 3) hydrogen bonds : bond 0.03168 ( 54) hydrogen bonds : angle 4.51443 ( 141) SS BOND : bond 0.00164 ( 1) SS BOND : angle 0.61765 ( 2) covalent geometry : bond 0.00301 ( 1162) covalent geometry : angle 0.75848 ( 1589) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.120 Fit side-chains REVERT: A 36 ILE cc_start: 0.8912 (mm) cc_final: 0.8656 (mt) outliers start: 1 outliers final: 1 residues processed: 17 average time/residue: 0.1772 time to fit residues: 3.3691 Evaluate side-chains 16 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 2 optimal weight: 0.0470 chunk 8 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.0670 chunk 4 optimal weight: 0.1980 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 0.0980 chunk 11 optimal weight: 0.5980 chunk 1 optimal weight: 0.0040 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.0828 ------------------------------------------------------------------------------- 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 = 0.3902 r_free = 0.3902 target = 0.167509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.145884 restraints weight = 1790.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.148705 restraints weight = 1184.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.150784 restraints weight = 898.455| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.5827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 1167 Z= 0.111 Angle : 0.722 11.481 1603 Z= 0.335 Chirality : 0.064 0.534 178 Planarity : 0.005 0.040 193 Dihedral : 5.892 29.994 235 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.23 % Allowed : 25.93 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.49 (0.75), residues: 129 helix: 5.25 (1.21), residues: 12 sheet: 0.78 (0.63), residues: 74 loop : -2.04 (0.73), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 201 HIS 0.001 0.000 HIS A 189 PHE 0.030 0.002 PHE A 39 TYR 0.005 0.001 TYR A 43 ARG 0.003 0.001 ARG A 194 Details of bonding type rmsd link_NAG-ASN : bond 0.01457 ( 3) link_NAG-ASN : angle 5.29147 ( 9) link_BETA1-4 : bond 0.00194 ( 1) link_BETA1-4 : angle 2.21148 ( 3) hydrogen bonds : bond 0.02743 ( 54) hydrogen bonds : angle 4.37525 ( 141) SS BOND : bond 0.00102 ( 1) SS BOND : angle 0.50661 ( 2) covalent geometry : bond 0.00238 ( 1162) covalent geometry : angle 0.59823 ( 1589) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.111 Fit side-chains REVERT: A 36 ILE cc_start: 0.8794 (mm) cc_final: 0.8557 (mt) outliers start: 1 outliers final: 1 residues processed: 17 average time/residue: 0.1542 time to fit residues: 2.9915 Evaluate side-chains 16 residues out of total 133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 5 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 8 optimal weight: 0.0970 chunk 1 optimal weight: 0.0070 chunk 6 optimal weight: 0.5980 chunk 10 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.0670 chunk 9 optimal weight: 0.2980 chunk 3 optimal weight: 0.0870 overall best weight: 0.1112 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.167186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.145609 restraints weight = 1768.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.148429 restraints weight = 1197.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.150445 restraints weight = 905.827| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.5875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1167 Z= 0.116 Angle : 0.708 12.365 1603 Z= 0.335 Chirality : 0.064 0.540 178 Planarity : 0.007 0.067 193 Dihedral : 5.428 28.082 235 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.47 % Allowed : 25.93 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.59 (0.75), residues: 129 helix: 5.27 (1.14), residues: 12 sheet: 0.88 (0.63), residues: 74 loop : -2.06 (0.74), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 201 HIS 0.000 0.000 HIS A 157 PHE 0.031 0.002 PHE A 39 TYR 0.004 0.001 TYR A 43 ARG 0.003 0.001 ARG A 194 Details of bonding type rmsd link_NAG-ASN : bond 0.00819 ( 3) link_NAG-ASN : angle 5.37511 ( 9) link_BETA1-4 : bond 0.00214 ( 1) link_BETA1-4 : angle 2.20334 ( 3) hydrogen bonds : bond 0.02867 ( 54) hydrogen bonds : angle 4.37120 ( 141) SS BOND : bond 0.00154 ( 1) SS BOND : angle 0.52977 ( 2) covalent geometry : bond 0.00257 ( 1162) covalent geometry : angle 0.57667 ( 1589) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1348.11 seconds wall clock time: 23 minutes 51.65 seconds (1431.65 seconds total)