Starting phenix.real_space_refine on Wed Sep 17 04:31:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xs3_38613/09_2025/8xs3_38613.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xs3_38613/09_2025/8xs3_38613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xs3_38613/09_2025/8xs3_38613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xs3_38613/09_2025/8xs3_38613.map" model { file = "/net/cci-nas-00/data/ceres_data/8xs3_38613/09_2025/8xs3_38613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xs3_38613/09_2025/8xs3_38613.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 2572 2.51 5 N 691 2.21 5 O 833 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 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: 4118 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1587 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 13, 'TRANS': 200} Chain breaks: 2 Chain: "B" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1680 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 13, 'TRANS': 204} Chain: "C" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 809 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain breaks: 2 Chain: "D" 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: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.12, per 1000 atoms: 0.27 Number of scatterers: 4118 At special positions: 0 Unit cell: (55.89, 79.35, 109.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 833 8.00 N 691 7.00 C 2572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 93 " distance=2.04 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG CYS B 200 " distance=2.04 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 61 " distance=2.03 Simple disulfide: pdb=" SG CYS C 76 " - pdb=" SG CYS C 110 " distance=2.03 Simple disulfide: pdb=" SG CYS C 101 " - pdb=" SG CYS C 125 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 301 " - " ASN C 94 " " NAG D 1 " - " ASN C 120 " Time building additional restraints: 0.40 Conformation dependent library (CDL) restraints added in 184.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 990 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 14 sheets defined 7.9% alpha, 41.5% 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 87 through 91 removed outlier: 3.857A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 199 Processing helix chain 'A' and resid 208 through 211 Processing helix chain 'B' and resid 127 through 133 Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'C' and resid 79 through 87 Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.573A pdb=" N GLY C 103 " --> pdb=" O SER C 100 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.504A pdb=" N ILE A 34 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ARG A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12 Processing sheet with id=AA4, first strand: chain 'A' and resid 127 through 131 removed outlier: 3.913A pdb=" N GLY A 146 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N TYR A 183 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 127 through 131 removed outlier: 3.913A pdb=" N GLY A 146 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N TYR A 183 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 158 through 161 Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 6 removed outlier: 3.576A pdb=" N ASP B 75 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.087A pdb=" N LEU B 11 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU B 42 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LEU B 51 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 120 through 124 removed outlier: 6.054A pdb=" N TYR B 179 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 150 through 156 Processing sheet with id=AB2, first strand: chain 'C' and resid 29 through 30 Processing sheet with id=AB3, first strand: chain 'C' and resid 43 through 45 Processing sheet with id=AB4, first strand: chain 'C' and resid 76 through 77 removed outlier: 3.767A pdb=" N TYR C 91 " --> pdb=" O CYS C 76 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 96 through 99 167 hydrogen bonds defined for protein. 417 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: 0.48 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1317 1.34 - 1.46: 1004 1.46 - 1.58: 1856 1.58 - 1.70: 0 1.70 - 1.82: 28 Bond restraints: 4205 Sorted by residual: bond pdb=" C PHE A 129 " pdb=" N PRO A 130 " ideal model delta sigma weight residual 1.335 1.319 0.016 8.70e-03 1.32e+04 3.53e+00 bond pdb=" C LYS A 208 " pdb=" N PRO A 209 " ideal model delta sigma weight residual 1.336 1.355 -0.020 1.08e-02 8.57e+03 3.27e+00 bond pdb=" C LEU A 131 " pdb=" N ALA A 132 " ideal model delta sigma weight residual 1.330 1.307 0.023 1.47e-02 4.63e+03 2.45e+00 bond pdb=" C3 NAG D 1 " pdb=" O3 NAG D 1 " ideal model delta sigma weight residual 1.403 1.433 -0.030 2.00e-02 2.50e+03 2.29e+00 bond pdb=" C3 NAG D 2 " pdb=" O3 NAG D 2 " ideal model delta sigma weight residual 1.403 1.431 -0.028 2.00e-02 2.50e+03 1.95e+00 ... (remaining 4200 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 5463 1.67 - 3.34: 219 3.34 - 5.01: 27 5.01 - 6.68: 3 6.68 - 8.35: 2 Bond angle restraints: 5714 Sorted by residual: angle pdb=" N ILE A 102 " pdb=" CA ILE A 102 " pdb=" C ILE A 102 " ideal model delta sigma weight residual 113.71 109.19 4.52 9.50e-01 1.11e+00 2.26e+01 angle pdb=" N LEU B 97 " pdb=" CA LEU B 97 " pdb=" C LEU B 97 " ideal model delta sigma weight residual 113.88 109.74 4.14 1.23e+00 6.61e-01 1.13e+01 angle pdb=" CA VAL C 93 " pdb=" C VAL C 93 " pdb=" N ASN C 94 " ideal model delta sigma weight residual 115.45 118.84 -3.39 1.18e+00 7.18e-01 8.27e+00 angle pdb=" C5 NAG D 1 " pdb=" C4 NAG D 1 " pdb=" O4 NAG D 1 " ideal model delta sigma weight residual 111.70 103.35 8.35 3.00e+00 1.11e-01 7.74e+00 angle pdb=" N ARG A 67 " pdb=" CA ARG A 67 " pdb=" C ARG A 67 " ideal model delta sigma weight residual 114.39 110.50 3.89 1.45e+00 4.76e-01 7.19e+00 ... (remaining 5709 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 2372 17.99 - 35.99: 165 35.99 - 53.98: 28 53.98 - 71.97: 9 71.97 - 89.96: 4 Dihedral angle restraints: 2578 sinusoidal: 1035 harmonic: 1543 Sorted by residual: dihedral pdb=" CA ASN B 143 " pdb=" C ASN B 143 " pdb=" N ASN B 144 " pdb=" CA ASN B 144 " ideal model delta harmonic sigma weight residual 180.00 160.27 19.73 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA TRP A 161 " pdb=" C TRP A 161 " pdb=" N ASN A 162 " pdb=" CA ASN A 162 " ideal model delta harmonic sigma weight residual -180.00 -161.32 -18.68 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ASN A 162 " pdb=" C ASN A 162 " pdb=" N SER A 163 " pdb=" CA SER A 163 " ideal model delta harmonic sigma weight residual 180.00 -161.34 -18.66 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 2575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 462 0.040 - 0.079: 129 0.079 - 0.119: 50 0.119 - 0.158: 15 0.158 - 0.198: 1 Chirality restraints: 657 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.57e+01 chirality pdb=" CA ASN C 120 " pdb=" N ASN C 120 " pdb=" C ASN C 120 " pdb=" CB ASN C 120 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.76e-01 chirality pdb=" C1 NAG C 301 " pdb=" ND2 ASN C 94 " pdb=" C2 NAG C 301 " pdb=" O5 NAG C 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.91e-01 ... (remaining 654 not shown) Planarity restraints: 729 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 301 " 0.322 2.00e-02 2.50e+03 2.73e-01 9.34e+02 pdb=" C7 NAG C 301 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG C 301 " 0.185 2.00e-02 2.50e+03 pdb=" N2 NAG C 301 " -0.475 2.00e-02 2.50e+03 pdb=" O7 NAG C 301 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " 0.295 2.00e-02 2.50e+03 2.55e-01 8.13e+02 pdb=" C7 NAG D 2 " -0.066 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.005 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " -0.438 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.205 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.260 2.00e-02 2.50e+03 2.20e-01 6.07e+02 pdb=" C7 NAG D 1 " -0.067 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.171 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.376 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.012 2.00e-02 2.50e+03 ... (remaining 726 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 85 2.65 - 3.21: 4023 3.21 - 3.78: 6293 3.78 - 4.34: 8188 4.34 - 4.90: 13446 Nonbonded interactions: 32035 Sorted by model distance: nonbonded pdb=" NE2 GLN A 6 " pdb=" O GLN A 112 " model vdw 2.090 3.120 nonbonded pdb=" OE1 GLU B 39 " pdb=" OH TYR B 41 " model vdw 2.178 3.040 nonbonded pdb=" O HIS A 171 " pdb=" OG SER A 187 " model vdw 2.201 3.040 nonbonded pdb=" NZ LYS A 216 " pdb=" O ARG A 217 " model vdw 2.203 3.120 nonbonded pdb=" NH1 ARG A 98 " pdb=" O ARG A 99 " model vdw 2.213 3.120 ... (remaining 32030 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.940 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 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 : 0.005 0.044 4214 Z= 0.246 Angle : 0.784 8.560 5735 Z= 0.445 Chirality : 0.045 0.198 657 Planarity : 0.017 0.273 727 Dihedral : 13.189 89.965 1570 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.00 (0.31), residues: 521 helix: -3.54 (0.53), residues: 29 sheet: -0.81 (0.33), residues: 204 loop : -2.83 (0.29), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 148 TYR 0.015 0.002 TYR B 146 PHE 0.013 0.001 PHE C 108 TRP 0.013 0.001 TRP B 40 HIS 0.002 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 4205) covalent geometry : angle 0.76531 ( 5714) SS BOND : bond 0.00433 ( 6) SS BOND : angle 0.86882 ( 12) hydrogen bonds : bond 0.15251 ( 146) hydrogen bonds : angle 8.58742 ( 417) link_BETA1-4 : bond 0.00111 ( 1) link_BETA1-4 : angle 5.89694 ( 3) link_NAG-ASN : bond 0.00756 ( 2) link_NAG-ASN : angle 3.28369 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8516 (mt-10) REVERT: B 173 ASP cc_start: 0.8339 (t0) cc_final: 0.8124 (t70) REVERT: B 191 ASP cc_start: 0.9434 (t70) cc_final: 0.9158 (t0) REVERT: B 217 ARG cc_start: 0.8380 (mtm180) cc_final: 0.8171 (mtm180) REVERT: C 75 MET cc_start: 0.7929 (mmt) cc_final: 0.6714 (mmm) REVERT: C 91 TYR cc_start: 0.8305 (m-80) cc_final: 0.7863 (m-10) REVERT: C 97 MET cc_start: 0.9148 (tmm) cc_final: 0.8743 (tmm) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1092 time to fit residues: 5.7030 Evaluate side-chains 30 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN A 178 GLN B 95 GLN C 58 ASN C 70 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.041051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.033094 restraints weight = 29705.223| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 5.89 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4214 Z= 0.175 Angle : 0.665 6.878 5735 Z= 0.335 Chirality : 0.044 0.135 657 Planarity : 0.004 0.051 727 Dihedral : 5.554 34.120 631 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.64 % Allowed : 12.15 % Favored : 87.21 % 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: -2.18 (0.33), residues: 521 helix: -2.00 (0.67), residues: 30 sheet: -0.30 (0.33), residues: 206 loop : -2.36 (0.32), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 148 TYR 0.013 0.002 TYR C 107 PHE 0.009 0.001 PHE A 153 TRP 0.009 0.001 TRP B 40 HIS 0.001 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 4205) covalent geometry : angle 0.64871 ( 5714) SS BOND : bond 0.00373 ( 6) SS BOND : angle 0.87451 ( 12) hydrogen bonds : bond 0.03742 ( 146) hydrogen bonds : angle 6.25478 ( 417) link_BETA1-4 : bond 0.00303 ( 1) link_BETA1-4 : angle 3.10339 ( 3) link_NAG-ASN : bond 0.00139 ( 2) link_NAG-ASN : angle 3.91369 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.9272 (mt-10) cc_final: 0.9070 (mt-10) REVERT: B 173 ASP cc_start: 0.8584 (t0) cc_final: 0.8155 (t0) REVERT: B 217 ARG cc_start: 0.8300 (mtm180) cc_final: 0.7870 (mtm180) REVERT: C 26 MET cc_start: 0.9077 (tpp) cc_final: 0.7824 (pmm) REVERT: C 75 MET cc_start: 0.7403 (mmt) cc_final: 0.6374 (mmm) REVERT: C 107 TYR cc_start: 0.8689 (m-80) cc_final: 0.8411 (m-80) outliers start: 3 outliers final: 2 residues processed: 36 average time/residue: 0.0895 time to fit residues: 4.0802 Evaluate side-chains 29 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain C residue 64 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 9 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 31 optimal weight: 0.0770 chunk 4 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.040536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.032617 restraints weight = 29980.942| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 5.97 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4214 Z= 0.197 Angle : 0.650 6.557 5735 Z= 0.329 Chirality : 0.043 0.130 657 Planarity : 0.005 0.053 727 Dihedral : 5.146 24.246 631 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.92 % Allowed : 13.22 % Favored : 84.86 % 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: -1.82 (0.34), residues: 521 helix: -1.37 (0.77), residues: 30 sheet: -0.19 (0.32), residues: 218 loop : -2.11 (0.34), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 87 TYR 0.013 0.002 TYR B 146 PHE 0.008 0.001 PHE C 108 TRP 0.010 0.001 TRP A 161 HIS 0.002 0.001 HIS B 204 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 4205) covalent geometry : angle 0.63797 ( 5714) SS BOND : bond 0.00409 ( 6) SS BOND : angle 0.92460 ( 12) hydrogen bonds : bond 0.03502 ( 146) hydrogen bonds : angle 5.98870 ( 417) link_BETA1-4 : bond 0.00425 ( 1) link_BETA1-4 : angle 3.42574 ( 3) link_NAG-ASN : bond 0.00128 ( 2) link_NAG-ASN : angle 2.86550 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.9301 (mt-10) cc_final: 0.9079 (mt-10) REVERT: B 173 ASP cc_start: 0.8536 (t0) cc_final: 0.8082 (t0) REVERT: B 217 ARG cc_start: 0.8254 (mtm180) cc_final: 0.7871 (mtm180) REVERT: C 26 MET cc_start: 0.9173 (tpp) cc_final: 0.7831 (pmm) REVERT: C 75 MET cc_start: 0.7502 (mmt) cc_final: 0.6455 (mmm) REVERT: C 87 ASP cc_start: 0.9006 (m-30) cc_final: 0.7881 (t0) REVERT: C 107 TYR cc_start: 0.8746 (m-80) cc_final: 0.8439 (m-80) outliers start: 9 outliers final: 5 residues processed: 36 average time/residue: 0.0673 time to fit residues: 3.3011 Evaluate side-chains 29 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 117 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 26 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN B 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.039825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.031970 restraints weight = 30258.957| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 5.75 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 4214 Z= 0.250 Angle : 0.699 6.979 5735 Z= 0.352 Chirality : 0.044 0.142 657 Planarity : 0.005 0.053 727 Dihedral : 5.338 20.448 631 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.56 % Allowed : 15.57 % Favored : 81.88 % 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: -1.60 (0.34), residues: 521 helix: -1.40 (0.76), residues: 30 sheet: 0.00 (0.33), residues: 218 loop : -1.98 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 87 TYR 0.015 0.002 TYR B 146 PHE 0.009 0.001 PHE A 153 TRP 0.010 0.002 TRP A 161 HIS 0.003 0.001 HIS B 204 Details of bonding type rmsd covalent geometry : bond 0.00561 ( 4205) covalent geometry : angle 0.68802 ( 5714) SS BOND : bond 0.00666 ( 6) SS BOND : angle 1.09708 ( 12) hydrogen bonds : bond 0.03638 ( 146) hydrogen bonds : angle 5.97855 ( 417) link_BETA1-4 : bond 0.00469 ( 1) link_BETA1-4 : angle 3.44895 ( 3) link_NAG-ASN : bond 0.00257 ( 2) link_NAG-ASN : angle 2.72158 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 24 time to evaluate : 0.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.9283 (mt-10) cc_final: 0.9048 (mt-10) REVERT: A 151 ASP cc_start: 0.8898 (t0) cc_final: 0.8697 (t0) REVERT: B 173 ASP cc_start: 0.8523 (t0) cc_final: 0.8068 (t0) REVERT: C 26 MET cc_start: 0.9186 (tpp) cc_final: 0.8433 (tpp) REVERT: C 75 MET cc_start: 0.7536 (mmt) cc_final: 0.6754 (mmm) REVERT: C 107 TYR cc_start: 0.8729 (m-80) cc_final: 0.8422 (m-80) outliers start: 12 outliers final: 9 residues processed: 35 average time/residue: 0.0443 time to fit residues: 2.2571 Evaluate side-chains 33 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 117 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 15 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.039899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.032270 restraints weight = 29665.255| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 5.69 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4214 Z= 0.193 Angle : 0.647 7.059 5735 Z= 0.327 Chirality : 0.043 0.138 657 Planarity : 0.004 0.053 727 Dihedral : 5.076 19.095 631 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.35 % Allowed : 16.84 % 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: -1.45 (0.35), residues: 521 helix: -1.13 (0.80), residues: 30 sheet: 0.11 (0.33), residues: 218 loop : -1.91 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 87 TYR 0.014 0.002 TYR B 146 PHE 0.007 0.001 PHE A 153 TRP 0.009 0.001 TRP A 161 HIS 0.002 0.001 HIS B 204 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 4205) covalent geometry : angle 0.63826 ( 5714) SS BOND : bond 0.00405 ( 6) SS BOND : angle 0.88734 ( 12) hydrogen bonds : bond 0.03235 ( 146) hydrogen bonds : angle 5.74241 ( 417) link_BETA1-4 : bond 0.00204 ( 1) link_BETA1-4 : angle 3.22691 ( 3) link_NAG-ASN : bond 0.00113 ( 2) link_NAG-ASN : angle 2.40783 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 27 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 ASP cc_start: 0.8484 (t0) cc_final: 0.8023 (t0) REVERT: C 26 MET cc_start: 0.9101 (tpp) cc_final: 0.8385 (tpp) REVERT: C 75 MET cc_start: 0.7606 (mmt) cc_final: 0.6812 (mmm) REVERT: C 87 ASP cc_start: 0.8946 (m-30) cc_final: 0.7864 (t0) REVERT: C 107 TYR cc_start: 0.8730 (m-80) cc_final: 0.8393 (m-80) outliers start: 11 outliers final: 9 residues processed: 37 average time/residue: 0.0361 time to fit residues: 2.0343 Evaluate side-chains 33 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 117 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 44 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 28 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.040951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.032913 restraints weight = 29977.633| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 5.95 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4214 Z= 0.130 Angle : 0.604 6.719 5735 Z= 0.304 Chirality : 0.043 0.133 657 Planarity : 0.004 0.053 727 Dihedral : 4.730 18.244 631 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.35 % Allowed : 17.48 % Favored : 80.17 % 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 (0.35), residues: 521 helix: -0.38 (0.87), residues: 30 sheet: 0.09 (0.33), residues: 223 loop : -1.69 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 87 TYR 0.013 0.001 TYR B 146 PHE 0.006 0.001 PHE A 153 TRP 0.010 0.002 TRP B 40 HIS 0.002 0.000 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 4205) covalent geometry : angle 0.59563 ( 5714) SS BOND : bond 0.00327 ( 6) SS BOND : angle 0.78414 ( 12) hydrogen bonds : bond 0.02812 ( 146) hydrogen bonds : angle 5.38890 ( 417) link_BETA1-4 : bond 0.00018 ( 1) link_BETA1-4 : angle 2.94054 ( 3) link_NAG-ASN : bond 0.00122 ( 2) link_NAG-ASN : angle 2.20844 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 25 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 ASP cc_start: 0.8488 (t0) cc_final: 0.8053 (t0) REVERT: C 26 MET cc_start: 0.9101 (tpp) cc_final: 0.8350 (tpp) REVERT: C 75 MET cc_start: 0.7515 (mmt) cc_final: 0.6634 (mmm) REVERT: C 87 ASP cc_start: 0.8984 (m-30) cc_final: 0.7869 (t0) REVERT: C 107 TYR cc_start: 0.8684 (m-80) cc_final: 0.8385 (m-80) outliers start: 11 outliers final: 9 residues processed: 35 average time/residue: 0.0474 time to fit residues: 2.4724 Evaluate side-chains 33 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 117 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 20 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 16 optimal weight: 0.4980 chunk 29 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.041450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.033375 restraints weight = 29795.750| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 6.05 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4214 Z= 0.110 Angle : 0.606 8.361 5735 Z= 0.298 Chirality : 0.042 0.130 657 Planarity : 0.004 0.054 727 Dihedral : 4.393 17.758 631 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.13 % Allowed : 18.12 % Favored : 79.74 % 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: -0.85 (0.36), residues: 521 helix: 0.45 (0.99), residues: 30 sheet: 0.40 (0.33), residues: 221 loop : -1.56 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 87 TYR 0.011 0.001 TYR B 146 PHE 0.006 0.001 PHE A 153 TRP 0.010 0.001 TRP B 40 HIS 0.001 0.000 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 4205) covalent geometry : angle 0.59950 ( 5714) SS BOND : bond 0.00275 ( 6) SS BOND : angle 0.69959 ( 12) hydrogen bonds : bond 0.02550 ( 146) hydrogen bonds : angle 5.07685 ( 417) link_BETA1-4 : bond 0.00076 ( 1) link_BETA1-4 : angle 2.62720 ( 3) link_NAG-ASN : bond 0.00126 ( 2) link_NAG-ASN : angle 2.01950 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9196 (tp) REVERT: A 202 ILE cc_start: 0.8771 (mp) cc_final: 0.8465 (tp) REVERT: B 173 ASP cc_start: 0.8418 (t0) cc_final: 0.7958 (t70) REVERT: B 176 ASP cc_start: 0.8889 (t0) cc_final: 0.8566 (t0) REVERT: C 26 MET cc_start: 0.9020 (tpp) cc_final: 0.8224 (tpp) REVERT: C 75 MET cc_start: 0.7525 (mmt) cc_final: 0.6675 (mmm) REVERT: C 87 ASP cc_start: 0.8907 (m-30) cc_final: 0.7781 (t0) REVERT: C 107 TYR cc_start: 0.8680 (m-80) cc_final: 0.8467 (m-80) outliers start: 10 outliers final: 8 residues processed: 38 average time/residue: 0.0639 time to fit residues: 3.3184 Evaluate side-chains 37 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 117 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 23 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.040383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.032386 restraints weight = 30182.181| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 5.98 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4214 Z= 0.193 Angle : 0.652 7.125 5735 Z= 0.324 Chirality : 0.043 0.129 657 Planarity : 0.004 0.055 727 Dihedral : 4.728 20.626 631 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.77 % Allowed : 18.34 % Favored : 78.89 % 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: -0.90 (0.36), residues: 521 helix: 0.28 (0.94), residues: 30 sheet: 0.33 (0.34), residues: 221 loop : -1.55 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 87 TYR 0.013 0.002 TYR B 146 PHE 0.008 0.001 PHE A 153 TRP 0.017 0.001 TRP A 161 HIS 0.003 0.001 HIS B 204 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 4205) covalent geometry : angle 0.64479 ( 5714) SS BOND : bond 0.00347 ( 6) SS BOND : angle 0.79976 ( 12) hydrogen bonds : bond 0.03041 ( 146) hydrogen bonds : angle 5.25365 ( 417) link_BETA1-4 : bond 0.00330 ( 1) link_BETA1-4 : angle 2.84241 ( 3) link_NAG-ASN : bond 0.00241 ( 2) link_NAG-ASN : angle 2.20225 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 25 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ILE cc_start: 0.8771 (mp) cc_final: 0.8446 (tp) REVERT: B 94 MET cc_start: 0.7929 (tmm) cc_final: 0.7729 (tmm) REVERT: B 173 ASP cc_start: 0.8457 (t0) cc_final: 0.8073 (t70) REVERT: C 26 MET cc_start: 0.9135 (tpp) cc_final: 0.8807 (tpp) REVERT: C 75 MET cc_start: 0.7604 (mmt) cc_final: 0.6821 (mmm) REVERT: C 87 ASP cc_start: 0.8967 (m-30) cc_final: 0.7867 (t0) REVERT: C 107 TYR cc_start: 0.8705 (m-80) cc_final: 0.8425 (m-80) outliers start: 13 outliers final: 11 residues processed: 37 average time/residue: 0.0482 time to fit residues: 2.6595 Evaluate side-chains 36 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 25 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 117 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 22 optimal weight: 0.0470 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.040437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.032504 restraints weight = 30421.891| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 5.98 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4214 Z= 0.169 Angle : 0.649 9.631 5735 Z= 0.319 Chirality : 0.043 0.127 657 Planarity : 0.004 0.054 727 Dihedral : 4.686 20.018 631 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.56 % Allowed : 18.55 % Favored : 78.89 % 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: -0.85 (0.36), residues: 521 helix: 0.44 (0.96), residues: 30 sheet: 0.36 (0.34), residues: 221 loop : -1.53 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 87 TYR 0.013 0.001 TYR B 146 PHE 0.006 0.001 PHE A 153 TRP 0.013 0.001 TRP A 161 HIS 0.002 0.001 HIS B 204 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 4205) covalent geometry : angle 0.64270 ( 5714) SS BOND : bond 0.00346 ( 6) SS BOND : angle 0.73667 ( 12) hydrogen bonds : bond 0.02964 ( 146) hydrogen bonds : angle 5.27855 ( 417) link_BETA1-4 : bond 0.00099 ( 1) link_BETA1-4 : angle 2.74447 ( 3) link_NAG-ASN : bond 0.00130 ( 2) link_NAG-ASN : angle 2.09185 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 25 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ILE cc_start: 0.8755 (mp) cc_final: 0.8441 (tp) REVERT: B 94 MET cc_start: 0.7916 (tmm) cc_final: 0.7698 (tmm) REVERT: B 173 ASP cc_start: 0.8440 (t0) cc_final: 0.8055 (t70) REVERT: C 26 MET cc_start: 0.9089 (tpp) cc_final: 0.8440 (tpp) REVERT: C 75 MET cc_start: 0.7616 (mmt) cc_final: 0.6826 (mmm) REVERT: C 87 ASP cc_start: 0.8971 (m-30) cc_final: 0.7860 (t0) REVERT: C 107 TYR cc_start: 0.8695 (m-80) cc_final: 0.8420 (m-80) outliers start: 12 outliers final: 11 residues processed: 36 average time/residue: 0.0495 time to fit residues: 2.6583 Evaluate side-chains 35 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 24 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 21 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN B 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.039243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.031705 restraints weight = 30480.935| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 5.69 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 4214 Z= 0.279 Angle : 0.732 8.863 5735 Z= 0.363 Chirality : 0.044 0.131 657 Planarity : 0.005 0.057 727 Dihedral : 5.247 21.983 631 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.99 % Allowed : 18.12 % Favored : 78.89 % 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: -1.06 (0.36), residues: 521 helix: -0.07 (0.88), residues: 30 sheet: 0.20 (0.34), residues: 223 loop : -1.61 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 87 TYR 0.015 0.002 TYR B 146 PHE 0.007 0.001 PHE A 153 TRP 0.021 0.002 TRP A 161 HIS 0.003 0.001 HIS B 204 Details of bonding type rmsd covalent geometry : bond 0.00626 ( 4205) covalent geometry : angle 0.72443 ( 5714) SS BOND : bond 0.00478 ( 6) SS BOND : angle 0.92970 ( 12) hydrogen bonds : bond 0.03547 ( 146) hydrogen bonds : angle 5.60742 ( 417) link_BETA1-4 : bond 0.00570 ( 1) link_BETA1-4 : angle 3.02517 ( 3) link_NAG-ASN : bond 0.00414 ( 2) link_NAG-ASN : angle 2.36580 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 25 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 MET cc_start: 0.8067 (tmm) cc_final: 0.7690 (tmm) REVERT: B 173 ASP cc_start: 0.8452 (t0) cc_final: 0.8009 (t0) REVERT: C 26 MET cc_start: 0.9099 (tpp) cc_final: 0.8766 (tpp) REVERT: C 75 MET cc_start: 0.7709 (mmt) cc_final: 0.6861 (mmm) REVERT: C 87 ASP cc_start: 0.8961 (m-30) cc_final: 0.7862 (t0) REVERT: C 107 TYR cc_start: 0.8757 (m-80) cc_final: 0.8449 (m-80) outliers start: 14 outliers final: 11 residues processed: 38 average time/residue: 0.0513 time to fit residues: 2.9698 Evaluate side-chains 35 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 24 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 0.0170 chunk 37 optimal weight: 0.4980 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.041513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.033310 restraints weight = 29324.580| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 6.11 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 4214 Z= 0.109 Angle : 0.620 9.189 5735 Z= 0.306 Chirality : 0.043 0.159 657 Planarity : 0.004 0.056 727 Dihedral : 4.463 17.564 631 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.92 % Allowed : 19.19 % Favored : 78.89 % 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: -0.68 (0.36), residues: 521 helix: 0.67 (1.02), residues: 30 sheet: 0.60 (0.34), residues: 218 loop : -1.53 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 87 TYR 0.012 0.001 TYR B 146 PHE 0.006 0.001 PHE A 153 TRP 0.015 0.001 TRP B 40 HIS 0.002 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 4205) covalent geometry : angle 0.61448 ( 5714) SS BOND : bond 0.00267 ( 6) SS BOND : angle 0.66811 ( 12) hydrogen bonds : bond 0.02614 ( 146) hydrogen bonds : angle 5.09445 ( 417) link_BETA1-4 : bond 0.00213 ( 1) link_BETA1-4 : angle 2.42268 ( 3) link_NAG-ASN : bond 0.00261 ( 2) link_NAG-ASN : angle 1.96546 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 924.71 seconds wall clock time: 16 minutes 47.72 seconds (1007.72 seconds total)