Starting phenix.real_space_refine on Wed Sep 17 04:06:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9neu_49336/09_2025/9neu_49336_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9neu_49336/09_2025/9neu_49336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9neu_49336/09_2025/9neu_49336.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9neu_49336/09_2025/9neu_49336.map" model { file = "/net/cci-nas-00/data/ceres_data/9neu_49336/09_2025/9neu_49336_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9neu_49336/09_2025/9neu_49336_neut.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.005 sd= 0.052 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 2340 2.51 5 N 640 2.21 5 O 664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3648 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 912 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 912 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 912 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 912 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 0.89, per 1000 atoms: 0.24 Number of scatterers: 3648 At special positions: 0 Unit cell: (72.21, 72.21, 54.78, 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 664 8.00 N 640 7.00 C 2340 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: 0.27 Conformation dependent library (CDL) restraints added in 122.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 824 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 4 sheets defined 42.1% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 112 through 117 Processing helix chain 'A' and resid 125 through 129 Processing helix chain 'A' and resid 148 through 159 removed outlier: 3.779A pdb=" N TYR A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 181 Processing helix chain 'A' and resid 183 through 194 Processing helix chain 'B' and resid 112 through 117 Processing helix chain 'B' and resid 125 through 129 Processing helix chain 'B' and resid 148 through 158 removed outlier: 3.776A pdb=" N TYR B 156 " --> pdb=" O ILE B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 181 Processing helix chain 'B' and resid 183 through 194 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'C' and resid 148 through 158 removed outlier: 3.778A pdb=" N TYR C 156 " --> pdb=" O ILE C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 181 Processing helix chain 'C' and resid 183 through 194 Processing helix chain 'D' and resid 112 through 117 Processing helix chain 'D' and resid 125 through 129 Processing helix chain 'D' and resid 148 through 158 removed outlier: 3.643A pdb=" N TYR D 156 " --> pdb=" O ILE D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 181 Processing helix chain 'D' and resid 183 through 193 Processing sheet with id=AA1, first strand: chain 'A' and resid 106 through 111 removed outlier: 3.664A pdb=" N GLU A 139 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 106 through 111 removed outlier: 3.628A pdb=" N GLU B 139 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 106 through 111 removed outlier: 3.639A pdb=" N GLU C 139 " --> pdb=" O ASP C 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 106 through 111 removed outlier: 3.652A pdb=" N GLU D 139 " --> pdb=" O ASP D 134 " (cutoff:3.500A) 145 hydrogen bonds defined for protein. 405 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: 0.39 Time building geometry restraints manager: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1232 1.34 - 1.46: 834 1.46 - 1.58: 1678 1.58 - 1.69: 0 1.69 - 1.81: 4 Bond restraints: 3748 Sorted by residual: bond pdb=" CB PRO C 119 " pdb=" CG PRO C 119 " ideal model delta sigma weight residual 1.492 1.541 -0.049 5.00e-02 4.00e+02 9.61e-01 bond pdb=" CB GLN C 84 " pdb=" CG GLN C 84 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 7.87e-01 bond pdb=" CA ASP D 120 " pdb=" CB ASP D 120 " ideal model delta sigma weight residual 1.517 1.537 -0.020 2.41e-02 1.72e+03 6.94e-01 bond pdb=" CA ASP B 120 " pdb=" CB ASP B 120 " ideal model delta sigma weight residual 1.517 1.536 -0.019 2.41e-02 1.72e+03 6.37e-01 bond pdb=" CA ASP A 120 " pdb=" CB ASP A 120 " ideal model delta sigma weight residual 1.517 1.536 -0.019 2.41e-02 1.72e+03 6.27e-01 ... (remaining 3743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 4771 1.07 - 2.14: 194 2.14 - 3.21: 69 3.21 - 4.28: 18 4.28 - 5.35: 16 Bond angle restraints: 5068 Sorted by residual: angle pdb=" C ASP D 120 " pdb=" CA ASP D 120 " pdb=" CB ASP D 120 " ideal model delta sigma weight residual 115.89 112.44 3.45 1.32e+00 5.74e-01 6.82e+00 angle pdb=" C ASP B 120 " pdb=" CA ASP B 120 " pdb=" CB ASP B 120 " ideal model delta sigma weight residual 115.89 112.47 3.42 1.32e+00 5.74e-01 6.73e+00 angle pdb=" C ASP A 120 " pdb=" CA ASP A 120 " pdb=" CB ASP A 120 " ideal model delta sigma weight residual 115.89 112.47 3.42 1.32e+00 5.74e-01 6.70e+00 angle pdb=" C PRO B 165 " pdb=" N VAL B 166 " pdb=" CA VAL B 166 " ideal model delta sigma weight residual 121.97 117.92 4.05 1.80e+00 3.09e-01 5.06e+00 angle pdb=" N ARG A 146 " pdb=" CA ARG A 146 " pdb=" C ARG A 146 " ideal model delta sigma weight residual 109.81 114.71 -4.90 2.21e+00 2.05e-01 4.92e+00 ... (remaining 5063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 2017 17.67 - 35.33: 198 35.33 - 53.00: 37 53.00 - 70.67: 0 70.67 - 88.33: 4 Dihedral angle restraints: 2256 sinusoidal: 984 harmonic: 1272 Sorted by residual: dihedral pdb=" CA VAL B 166 " pdb=" C VAL B 166 " pdb=" N ASN B 167 " pdb=" CA ASN B 167 " ideal model delta harmonic sigma weight residual 180.00 162.66 17.34 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA VAL D 166 " pdb=" C VAL D 166 " pdb=" N ASN D 167 " pdb=" CA ASN D 167 " ideal model delta harmonic sigma weight residual 180.00 163.67 16.33 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA PHE C 118 " pdb=" C PHE C 118 " pdb=" N PRO C 119 " pdb=" CA PRO C 119 " ideal model delta harmonic sigma weight residual 180.00 163.71 16.29 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 2253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 288 0.025 - 0.051: 119 0.051 - 0.076: 58 0.076 - 0.102: 26 0.102 - 0.127: 21 Chirality restraints: 512 Sorted by residual: chirality pdb=" CA ARG B 146 " pdb=" N ARG B 146 " pdb=" C ARG B 146 " pdb=" CB ARG B 146 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.03e-01 chirality pdb=" CA ARG C 146 " pdb=" N ARG C 146 " pdb=" C ARG C 146 " pdb=" CB ARG C 146 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.69e-01 chirality pdb=" CA ARG A 146 " pdb=" N ARG A 146 " pdb=" C ARG A 146 " pdb=" CB ARG A 146 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.67e-01 ... (remaining 509 not shown) Planarity restraints: 684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 118 " -0.061 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO C 119 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO C 119 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 119 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 168 " 0.028 5.00e-02 4.00e+02 4.24e-02 2.87e+00 pdb=" N PRO C 169 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 169 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 169 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 168 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.71e+00 pdb=" N PRO B 169 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 169 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 169 " -0.023 5.00e-02 4.00e+02 ... (remaining 681 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1136 2.83 - 3.34: 3277 3.34 - 3.86: 6177 3.86 - 4.38: 7310 4.38 - 4.90: 12513 Nonbonded interactions: 30413 Sorted by model distance: nonbonded pdb=" O TYR C 154 " pdb=" OG SER C 158 " model vdw 2.307 3.040 nonbonded pdb=" O TYR B 154 " pdb=" OG SER B 158 " model vdw 2.314 3.040 nonbonded pdb=" O TYR A 154 " pdb=" OG SER A 158 " model vdw 2.314 3.040 nonbonded pdb=" O TYR D 154 " pdb=" OG SER D 158 " model vdw 2.317 3.040 nonbonded pdb=" O ASP C 120 " pdb=" OG1 THR C 121 " model vdw 2.356 3.040 ... (remaining 30408 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 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: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.180 Find NCS groups from input model: 0.040 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:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 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 : 0.003 0.049 3748 Z= 0.142 Angle : 0.632 5.352 5068 Z= 0.316 Chirality : 0.042 0.127 512 Planarity : 0.006 0.091 684 Dihedral : 14.229 88.335 1432 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.36), residues: 416 helix: 0.99 (0.45), residues: 144 sheet: 1.08 (0.61), residues: 40 loop : -1.67 (0.31), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 163 TYR 0.006 0.001 TYR D 155 PHE 0.006 0.001 PHE B 108 HIS 0.001 0.000 HIS A 91 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 3748) covalent geometry : angle 0.63179 ( 5068) hydrogen bonds : bond 0.21928 ( 145) hydrogen bonds : angle 6.70129 ( 405) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.5374 time to fit residues: 57.6470 Evaluate side-chains 92 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.0470 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 167 ASN B 111 GLN B 167 ASN C 111 GLN C 167 ASN D 111 GLN D 167 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.164721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.128478 restraints weight = 4087.529| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.62 r_work: 0.3288 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3748 Z= 0.164 Angle : 0.654 5.314 5068 Z= 0.335 Chirality : 0.047 0.124 512 Planarity : 0.006 0.065 684 Dihedral : 3.893 17.196 496 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.76 % Allowed : 11.36 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.38), residues: 416 helix: 1.00 (0.44), residues: 144 sheet: 1.61 (0.70), residues: 40 loop : -1.49 (0.35), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 107 TYR 0.010 0.001 TYR A 154 PHE 0.010 0.001 PHE D 173 HIS 0.001 0.000 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 3748) covalent geometry : angle 0.65426 ( 5068) hydrogen bonds : bond 0.04608 ( 145) hydrogen bonds : angle 4.73542 ( 405) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 0.168 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 104 average time/residue: 0.5440 time to fit residues: 58.2625 Evaluate side-chains 96 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 0.0370 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 167 ASN B 111 GLN B 167 ASN C 111 GLN C 167 ASN D 111 GLN D 167 ASN D 188 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.165402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.128793 restraints weight = 3989.803| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.62 r_work: 0.3305 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3748 Z= 0.158 Angle : 0.643 4.954 5068 Z= 0.331 Chirality : 0.046 0.126 512 Planarity : 0.006 0.058 684 Dihedral : 3.910 18.173 496 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.52 % Allowed : 17.68 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.39), residues: 416 helix: 1.00 (0.44), residues: 144 sheet: 1.80 (0.73), residues: 40 loop : -1.43 (0.36), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 161 TYR 0.008 0.001 TYR A 154 PHE 0.009 0.001 PHE B 173 HIS 0.001 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 3748) covalent geometry : angle 0.64317 ( 5068) hydrogen bonds : bond 0.04244 ( 145) hydrogen bonds : angle 4.60468 ( 405) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 163 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.8030 (mtt180) outliers start: 6 outliers final: 5 residues processed: 105 average time/residue: 0.5605 time to fit residues: 60.5206 Evaluate side-chains 99 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 163 ARG Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain D residue 130 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 13 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 27 optimal weight: 0.2980 chunk 20 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 167 ASN B 111 GLN B 167 ASN C 111 GLN C 167 ASN D 111 GLN D 167 ASN D 188 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.161289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.124037 restraints weight = 4019.541| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.64 r_work: 0.3266 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 3748 Z= 0.242 Angle : 0.706 5.062 5068 Z= 0.369 Chirality : 0.050 0.124 512 Planarity : 0.007 0.053 684 Dihedral : 4.347 20.447 496 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 4.04 % Allowed : 17.17 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.38), residues: 416 helix: 0.30 (0.41), residues: 168 sheet: 1.82 (0.78), residues: 40 loop : -2.37 (0.34), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 107 TYR 0.008 0.002 TYR B 154 PHE 0.010 0.001 PHE C 173 HIS 0.002 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00583 ( 3748) covalent geometry : angle 0.70600 ( 5068) hydrogen bonds : bond 0.04637 ( 145) hydrogen bonds : angle 4.90700 ( 405) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7842 (mtt180) REVERT: C 163 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8067 (mtt180) outliers start: 16 outliers final: 8 residues processed: 106 average time/residue: 0.6748 time to fit residues: 73.2465 Evaluate side-chains 105 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 163 ARG Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 146 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 167 ASN B 111 GLN B 167 ASN B 188 ASN C 111 GLN C 167 ASN C 188 ASN D 111 GLN D 167 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.163436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.126390 restraints weight = 4034.351| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.65 r_work: 0.3290 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3748 Z= 0.188 Angle : 0.675 5.170 5068 Z= 0.350 Chirality : 0.048 0.134 512 Planarity : 0.006 0.050 684 Dihedral : 4.242 18.945 496 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 3.54 % Allowed : 19.19 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.38), residues: 416 helix: 0.11 (0.40), residues: 168 sheet: 1.72 (0.76), residues: 40 loop : -2.34 (0.35), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 107 TYR 0.008 0.001 TYR A 154 PHE 0.010 0.001 PHE B 173 HIS 0.001 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 3748) covalent geometry : angle 0.67472 ( 5068) hydrogen bonds : bond 0.04283 ( 145) hydrogen bonds : angle 4.80814 ( 405) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7877 (mtt180) REVERT: C 163 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.8031 (mtt180) outliers start: 14 outliers final: 8 residues processed: 99 average time/residue: 0.6564 time to fit residues: 66.6696 Evaluate side-chains 101 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 163 ARG Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 146 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 2 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 4 optimal weight: 0.1980 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 167 ASN B 111 GLN B 167 ASN C 111 GLN C 167 ASN D 111 GLN D 167 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.164869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.128121 restraints weight = 4027.305| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.65 r_work: 0.3304 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3748 Z= 0.158 Angle : 0.657 5.361 5068 Z= 0.339 Chirality : 0.047 0.144 512 Planarity : 0.006 0.038 684 Dihedral : 4.037 17.833 496 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 3.79 % Allowed : 20.20 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.38), residues: 416 helix: 0.23 (0.41), residues: 168 sheet: 1.61 (0.74), residues: 40 loop : -2.30 (0.35), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 107 TYR 0.008 0.001 TYR A 154 PHE 0.010 0.001 PHE B 173 HIS 0.001 0.001 HIS D 85 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 3748) covalent geometry : angle 0.65664 ( 5068) hydrogen bonds : bond 0.04031 ( 145) hydrogen bonds : angle 4.61028 ( 405) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 163 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.8005 (mtt180) outliers start: 15 outliers final: 6 residues processed: 103 average time/residue: 0.5936 time to fit residues: 62.9133 Evaluate side-chains 97 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 163 ARG Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 163 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 37 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 167 ASN B 111 GLN B 167 ASN C 111 GLN C 167 ASN D 111 GLN D 167 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.163512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.126551 restraints weight = 4075.866| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.66 r_work: 0.3290 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3748 Z= 0.181 Angle : 0.677 5.473 5068 Z= 0.349 Chirality : 0.049 0.155 512 Planarity : 0.006 0.036 684 Dihedral : 4.094 17.982 496 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 3.28 % Allowed : 22.47 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.38), residues: 416 helix: 0.20 (0.41), residues: 168 sheet: 1.54 (0.74), residues: 40 loop : -2.30 (0.36), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 107 TYR 0.008 0.001 TYR A 154 PHE 0.010 0.001 PHE B 173 HIS 0.001 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 3748) covalent geometry : angle 0.67684 ( 5068) hydrogen bonds : bond 0.04199 ( 145) hydrogen bonds : angle 4.62375 ( 405) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 163 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.8045 (mtt180) REVERT: D 163 ARG cc_start: 0.8164 (ptp-110) cc_final: 0.7688 (ptm160) outliers start: 13 outliers final: 8 residues processed: 98 average time/residue: 0.6723 time to fit residues: 67.6246 Evaluate side-chains 101 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 163 ARG Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain D residue 146 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 7 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 chunk 2 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN B 111 GLN B 167 ASN C 111 GLN C 167 ASN D 111 GLN D 167 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.166767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.131862 restraints weight = 4050.518| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.55 r_work: 0.3333 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3748 Z= 0.159 Angle : 0.686 6.251 5068 Z= 0.351 Chirality : 0.048 0.165 512 Planarity : 0.005 0.034 684 Dihedral : 3.970 17.437 496 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 2.78 % Allowed : 23.48 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.39), residues: 416 helix: 0.20 (0.41), residues: 168 sheet: 1.58 (0.74), residues: 40 loop : -2.27 (0.36), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 107 TYR 0.008 0.001 TYR A 154 PHE 0.010 0.001 PHE A 173 HIS 0.001 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 3748) covalent geometry : angle 0.68566 ( 5068) hydrogen bonds : bond 0.04054 ( 145) hydrogen bonds : angle 4.50778 ( 405) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 163 ARG cc_start: 0.8118 (ptp-110) cc_final: 0.7615 (ptm160) outliers start: 11 outliers final: 8 residues processed: 104 average time/residue: 0.6151 time to fit residues: 65.7207 Evaluate side-chains 101 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 163 ARG Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain D residue 146 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 38 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN B 111 GLN B 167 ASN C 111 GLN C 167 ASN D 111 GLN D 167 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.164237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.127009 restraints weight = 4021.775| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.65 r_work: 0.3284 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3748 Z= 0.182 Angle : 0.702 6.718 5068 Z= 0.361 Chirality : 0.050 0.187 512 Planarity : 0.006 0.034 684 Dihedral : 4.051 17.510 496 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 3.28 % Allowed : 23.99 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.39), residues: 416 helix: 0.17 (0.41), residues: 168 sheet: 1.53 (0.74), residues: 40 loop : -2.28 (0.36), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 107 TYR 0.007 0.001 TYR A 155 PHE 0.009 0.001 PHE C 173 HIS 0.001 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 3748) covalent geometry : angle 0.70174 ( 5068) hydrogen bonds : bond 0.04208 ( 145) hydrogen bonds : angle 4.59353 ( 405) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 163 ARG cc_start: 0.8182 (ptp-110) cc_final: 0.7944 (ptp-170) outliers start: 13 outliers final: 8 residues processed: 98 average time/residue: 0.6502 time to fit residues: 65.3198 Evaluate side-chains 102 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 163 ARG Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain D residue 146 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 10 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 167 ASN B 111 GLN B 167 ASN C 111 GLN C 167 ASN D 167 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.164364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.132528 restraints weight = 4064.037| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.29 r_work: 0.3336 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 3748 Z= 0.202 Angle : 0.744 7.159 5068 Z= 0.382 Chirality : 0.051 0.207 512 Planarity : 0.006 0.034 684 Dihedral : 4.136 18.897 496 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 2.78 % Allowed : 25.00 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.38), residues: 416 helix: 0.10 (0.41), residues: 168 sheet: 1.50 (0.74), residues: 40 loop : -2.29 (0.36), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 107 TYR 0.008 0.001 TYR B 154 PHE 0.009 0.001 PHE B 173 HIS 0.001 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 3748) covalent geometry : angle 0.74428 ( 5068) hydrogen bonds : bond 0.04348 ( 145) hydrogen bonds : angle 4.66832 ( 405) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 163 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7998 (mtt180) REVERT: D 163 ARG cc_start: 0.8173 (ptp-110) cc_final: 0.7917 (ptp-170) outliers start: 11 outliers final: 7 residues processed: 98 average time/residue: 0.6049 time to fit residues: 60.8228 Evaluate side-chains 102 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 163 ARG Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain D residue 146 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 167 ASN B 111 GLN B 167 ASN C 111 GLN C 167 ASN D 111 GLN D 167 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.164996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.130656 restraints weight = 3977.165| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.44 r_work: 0.3326 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3748 Z= 0.190 Angle : 0.731 6.945 5068 Z= 0.376 Chirality : 0.051 0.201 512 Planarity : 0.006 0.035 684 Dihedral : 4.129 18.843 496 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 3.28 % Allowed : 24.24 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.38), residues: 416 helix: 0.07 (0.40), residues: 168 sheet: 1.53 (0.74), residues: 40 loop : -2.31 (0.36), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 107 TYR 0.008 0.001 TYR B 154 PHE 0.009 0.001 PHE B 173 HIS 0.001 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 3748) covalent geometry : angle 0.73124 ( 5068) hydrogen bonds : bond 0.04302 ( 145) hydrogen bonds : angle 4.64774 ( 405) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1650.23 seconds wall clock time: 28 minutes 55.83 seconds (1735.83 seconds total)