Starting phenix.real_space_refine on Thu Mar 6 00:25:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xs3_38613/03_2025/8xs3_38613.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xs3_38613/03_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_38613/03_2025/8xs3_38613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xs3_38613/03_2025/8xs3_38613.map" model { file = "/net/cci-nas-00/data/ceres_data/8xs3_38613/03_2025/8xs3_38613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xs3_38613/03_2025/8xs3_38613.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 3.71, per 1000 atoms: 0.90 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: 1.09 Conformation dependent library (CDL) restraints added in 555.8 milliseconds 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: 0.57 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: 1.18 Time building geometry restraints manager: 1.29 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: 3.600 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.560 Find NCS groups from input model: 0.050 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:3.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.170 ------------------------------------------------------------------------------- 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 4205 Z= 0.314 Angle : 0.765 8.346 5714 Z= 0.442 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 : 16.27 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.013 0.001 TRP B 40 HIS 0.002 0.001 HIS B 195 PHE 0.013 0.001 PHE C 108 TYR 0.015 0.002 TYR B 146 ARG 0.005 0.000 ARG B 148 *********************** 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 : 0.477 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: 0.2331 time to fit residues: 12.2395 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 : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 0.5980 chunk 39 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 13 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 24 optimal weight: 0.3980 chunk 30 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 A 204 ASN B 95 GLN C 58 ASN C 70 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.041201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.033143 restraints weight = 29297.089| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 5.96 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4205 Z= 0.230 Angle : 0.645 6.537 5714 Z= 0.329 Chirality : 0.044 0.139 657 Planarity : 0.004 0.051 727 Dihedral : 5.590 34.869 631 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.64 % Allowed : 10.87 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.33), residues: 521 helix: -1.99 (0.66), residues: 30 sheet: -0.39 (0.33), residues: 210 loop : -2.32 (0.32), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 40 HIS 0.001 0.000 HIS B 195 PHE 0.009 0.001 PHE A 153 TYR 0.013 0.002 TYR C 107 ARG 0.003 0.001 ARG B 114 *********************** 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 : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 ASP cc_start: 0.8572 (t0) cc_final: 0.8142 (t0) REVERT: B 217 ARG cc_start: 0.8294 (mtm180) cc_final: 0.7873 (mtm180) REVERT: C 26 MET cc_start: 0.9060 (tpp) cc_final: 0.7841 (pmm) REVERT: C 75 MET cc_start: 0.7363 (mmt) cc_final: 0.6338 (mmm) REVERT: C 107 TYR cc_start: 0.8672 (m-80) cc_final: 0.8372 (m-80) outliers start: 3 outliers final: 2 residues processed: 36 average time/residue: 0.2803 time to fit residues: 13.0011 Evaluate side-chains 28 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 22 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.0020 chunk 21 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 overall best weight: 2.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.040397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.032532 restraints weight = 29807.849| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 5.89 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 4205 Z= 0.303 Angle : 0.649 6.576 5714 Z= 0.332 Chirality : 0.043 0.127 657 Planarity : 0.005 0.052 727 Dihedral : 5.198 24.071 631 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.92 % Allowed : 12.58 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.34), residues: 521 helix: -1.40 (0.77), residues: 30 sheet: -0.18 (0.32), residues: 218 loop : -2.10 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 161 HIS 0.002 0.001 HIS B 204 PHE 0.009 0.001 PHE C 108 TYR 0.013 0.002 TYR B 146 ARG 0.006 0.001 ARG A 87 *********************** 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 34 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.9161 (OUTLIER) cc_final: 0.8922 (pt0) REVERT: B 173 ASP cc_start: 0.8532 (t0) cc_final: 0.8079 (t0) REVERT: B 217 ARG cc_start: 0.8216 (mtm180) cc_final: 0.7835 (mtm180) REVERT: C 26 MET cc_start: 0.9191 (tpp) cc_final: 0.7809 (pmm) REVERT: C 75 MET cc_start: 0.7476 (mmt) cc_final: 0.6432 (mmm) REVERT: C 107 TYR cc_start: 0.8710 (m-80) cc_final: 0.8407 (m-80) outliers start: 9 outliers final: 5 residues processed: 34 average time/residue: 0.1510 time to fit residues: 7.0089 Evaluate side-chains 29 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU 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 2 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 12 optimal weight: 0.2980 chunk 15 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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 = 0.3108 r_free = 0.3108 target = 0.040448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.032557 restraints weight = 29988.289| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 5.82 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4205 Z= 0.267 Angle : 0.629 7.457 5714 Z= 0.320 Chirality : 0.043 0.145 657 Planarity : 0.004 0.052 727 Dihedral : 5.026 19.269 631 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.35 % Allowed : 15.57 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.34), residues: 521 helix: -1.05 (0.80), residues: 30 sheet: 0.07 (0.33), residues: 218 loop : -1.92 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 40 HIS 0.002 0.001 HIS B 204 PHE 0.008 0.001 PHE A 153 TYR 0.013 0.002 TYR B 146 ARG 0.005 0.000 ARG A 87 *********************** 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: 11 poor density : 25 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.8930 (pt0) REVERT: B 173 ASP cc_start: 0.8502 (t0) cc_final: 0.8052 (t0) REVERT: C 26 MET cc_start: 0.9135 (tpp) cc_final: 0.7662 (pmm) REVERT: C 66 TRP cc_start: 0.8525 (m100) cc_final: 0.8125 (m100) REVERT: C 75 MET cc_start: 0.7537 (mmt) cc_final: 0.6769 (mmm) REVERT: C 87 ASP cc_start: 0.8991 (m-30) cc_final: 0.7878 (t0) REVERT: C 107 TYR cc_start: 0.8728 (m-80) cc_final: 0.8399 (m-80) outliers start: 11 outliers final: 7 residues processed: 35 average time/residue: 0.1221 time to fit residues: 6.2164 Evaluate side-chains 32 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 46 GLU 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 23 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 64 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 35 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 = 0.3100 r_free = 0.3100 target = 0.039973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.032279 restraints weight = 30321.528| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 5.88 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4205 Z= 0.283 Angle : 0.637 6.903 5714 Z= 0.322 Chirality : 0.043 0.129 657 Planarity : 0.004 0.053 727 Dihedral : 4.980 19.307 631 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.99 % Allowed : 15.78 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.35), residues: 521 helix: -0.86 (0.82), residues: 30 sheet: 0.18 (0.33), residues: 218 loop : -1.82 (0.36), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 161 HIS 0.002 0.001 HIS B 204 PHE 0.008 0.001 PHE A 153 TYR 0.014 0.002 TYR B 146 ARG 0.004 0.000 ARG A 87 *********************** 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 40 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 26 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.9125 (OUTLIER) cc_final: 0.8912 (pt0) REVERT: B 173 ASP cc_start: 0.8473 (t0) cc_final: 0.8013 (t0) REVERT: C 26 MET cc_start: 0.9125 (tpp) cc_final: 0.8323 (tpp) REVERT: C 75 MET cc_start: 0.7604 (mmt) cc_final: 0.6809 (mmm) REVERT: C 87 ASP cc_start: 0.8930 (m-30) cc_final: 0.7818 (t0) REVERT: C 107 TYR cc_start: 0.8743 (m-80) cc_final: 0.8416 (m-80) outliers start: 14 outliers final: 9 residues processed: 39 average time/residue: 0.1178 time to fit residues: 6.6701 Evaluate side-chains 34 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 24 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 46 GLU 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 32 optimal weight: 0.7980 chunk 40 optimal weight: 0.2980 chunk 21 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 = 0.3118 r_free = 0.3118 target = 0.040777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.032935 restraints weight = 29203.543| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 5.89 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4205 Z= 0.212 Angle : 0.616 8.239 5714 Z= 0.307 Chirality : 0.042 0.144 657 Planarity : 0.004 0.053 727 Dihedral : 4.696 18.499 631 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.35 % Allowed : 17.27 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.35), residues: 521 helix: -0.19 (0.88), residues: 30 sheet: 0.30 (0.33), residues: 218 loop : -1.71 (0.36), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 40 HIS 0.002 0.001 HIS A 171 PHE 0.007 0.001 PHE A 153 TYR 0.013 0.001 TYR B 146 ARG 0.003 0.000 ARG A 87 *********************** 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 37 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 26 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9186 (tp) REVERT: B 173 ASP cc_start: 0.8477 (t0) cc_final: 0.8077 (t70) REVERT: C 26 MET cc_start: 0.9105 (tpp) cc_final: 0.8346 (tpp) REVERT: C 75 MET cc_start: 0.7519 (mmt) cc_final: 0.6638 (mmm) REVERT: C 87 ASP cc_start: 0.8950 (m-30) cc_final: 0.7828 (t0) REVERT: C 107 TYR cc_start: 0.8702 (m-80) cc_final: 0.8386 (m-80) outliers start: 11 outliers final: 7 residues processed: 36 average time/residue: 0.1160 time to fit residues: 6.1310 Evaluate side-chains 31 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 32 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3140 r_free = 0.3140 target = 0.041637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.033440 restraints weight = 29293.389| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 6.08 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4205 Z= 0.154 Angle : 0.593 7.954 5714 Z= 0.295 Chirality : 0.042 0.138 657 Planarity : 0.004 0.054 727 Dihedral : 4.353 17.499 631 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.92 % Allowed : 17.48 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.36), residues: 521 helix: 0.50 (1.00), residues: 30 sheet: 0.47 (0.34), residues: 221 loop : -1.50 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 40 HIS 0.001 0.000 HIS A 207 PHE 0.006 0.001 PHE A 153 TYR 0.011 0.001 TYR B 146 ARG 0.002 0.000 ARG A 87 *********************** 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 35 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 ASP cc_start: 0.8415 (t0) cc_final: 0.7965 (t70) REVERT: B 176 ASP cc_start: 0.8885 (t0) cc_final: 0.8579 (t0) REVERT: C 26 MET cc_start: 0.9043 (tpp) cc_final: 0.8239 (tpp) REVERT: C 75 MET cc_start: 0.7543 (mmt) cc_final: 0.6686 (mmm) REVERT: C 87 ASP cc_start: 0.8893 (m-30) cc_final: 0.7783 (t0) REVERT: C 107 TYR cc_start: 0.8708 (m-80) cc_final: 0.8473 (m-80) outliers start: 9 outliers final: 8 residues processed: 35 average time/residue: 0.1388 time to fit residues: 6.6833 Evaluate side-chains 34 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 202 ILE 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 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 14 optimal weight: 0.1980 chunk 34 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.041847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.033875 restraints weight = 29312.786| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 5.90 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4205 Z= 0.152 Angle : 0.587 7.789 5714 Z= 0.292 Chirality : 0.042 0.135 657 Planarity : 0.004 0.053 727 Dihedral : 4.198 17.545 631 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.13 % Allowed : 17.27 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.36), residues: 521 helix: 0.75 (1.03), residues: 30 sheet: 0.65 (0.34), residues: 218 loop : -1.42 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 40 HIS 0.001 0.000 HIS A 171 PHE 0.006 0.001 PHE A 153 TYR 0.011 0.001 TYR B 146 ARG 0.002 0.000 ARG A 87 *********************** 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 36 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 MET cc_start: 0.7794 (tmm) cc_final: 0.7547 (tmm) REVERT: B 173 ASP cc_start: 0.8372 (t0) cc_final: 0.7896 (t0) REVERT: B 176 ASP cc_start: 0.8879 (t0) cc_final: 0.8534 (t0) REVERT: C 26 MET cc_start: 0.9001 (tpp) cc_final: 0.8150 (tpp) REVERT: C 75 MET cc_start: 0.7517 (mmt) cc_final: 0.6647 (mmm) REVERT: C 87 ASP cc_start: 0.8868 (m-30) cc_final: 0.7776 (t0) REVERT: C 91 TYR cc_start: 0.8055 (m-80) cc_final: 0.7593 (m-10) REVERT: C 107 TYR cc_start: 0.8683 (m-80) cc_final: 0.8478 (m-80) outliers start: 10 outliers final: 9 residues processed: 35 average time/residue: 0.1386 time to fit residues: 6.6962 Evaluate side-chains 35 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 27 optimal weight: 0.1980 chunk 21 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.040445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.032623 restraints weight = 29942.644| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 5.82 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4205 Z= 0.288 Angle : 0.647 7.207 5714 Z= 0.323 Chirality : 0.042 0.132 657 Planarity : 0.004 0.054 727 Dihedral : 4.624 20.780 631 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.13 % Allowed : 17.27 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.36), residues: 521 helix: 0.59 (0.97), residues: 30 sheet: 0.47 (0.34), residues: 221 loop : -1.44 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 161 HIS 0.003 0.001 HIS B 204 PHE 0.006 0.001 PHE A 153 TYR 0.013 0.001 TYR B 146 ARG 0.004 0.000 ARG A 87 *********************** 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 34 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 24 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 MET cc_start: 0.7884 (tmm) cc_final: 0.7642 (tmm) REVERT: B 173 ASP cc_start: 0.8384 (t0) cc_final: 0.8003 (t70) REVERT: C 26 MET cc_start: 0.9095 (tpp) cc_final: 0.8757 (tpp) REVERT: C 75 MET cc_start: 0.7561 (mmt) cc_final: 0.6772 (mmm) REVERT: C 87 ASP cc_start: 0.8976 (m-30) cc_final: 0.7886 (t0) REVERT: C 107 TYR cc_start: 0.8706 (m-80) cc_final: 0.8466 (m-80) outliers start: 10 outliers final: 10 residues processed: 33 average time/residue: 0.1187 time to fit residues: 6.3186 Evaluate side-chains 34 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 24 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 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 42 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.040477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.032804 restraints weight = 29282.822| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 5.74 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4205 Z= 0.265 Angle : 0.644 8.856 5714 Z= 0.321 Chirality : 0.042 0.132 657 Planarity : 0.004 0.054 727 Dihedral : 4.682 20.425 631 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.35 % Allowed : 17.27 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.36), residues: 521 helix: 0.52 (0.97), residues: 30 sheet: 0.43 (0.34), residues: 223 loop : -1.42 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 161 HIS 0.003 0.001 HIS B 204 PHE 0.006 0.001 PHE A 153 TYR 0.014 0.001 TYR B 146 ARG 0.004 0.000 ARG A 87 ********************** 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 35 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 24 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 MET cc_start: 0.7938 (tmm) cc_final: 0.7693 (tmm) REVERT: B 173 ASP cc_start: 0.8432 (t0) cc_final: 0.8055 (t70) REVERT: C 26 MET cc_start: 0.9059 (tpp) cc_final: 0.8071 (mpp) REVERT: C 75 MET cc_start: 0.7696 (mmt) cc_final: 0.6887 (mmm) REVERT: C 87 ASP cc_start: 0.8937 (m-30) cc_final: 0.7825 (t0) REVERT: C 107 TYR cc_start: 0.8708 (m-80) cc_final: 0.8441 (m-80) outliers start: 11 outliers final: 11 residues processed: 34 average time/residue: 0.1102 time to fit residues: 5.5545 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 : 0.469 ------------------------------------------------------------------------------- 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 10 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.040612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.032927 restraints weight = 29167.386| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 5.75 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4205 Z= 0.244 Angle : 0.632 8.912 5714 Z= 0.315 Chirality : 0.042 0.131 657 Planarity : 0.004 0.055 727 Dihedral : 4.699 20.443 631 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.13 % Allowed : 17.91 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.36), residues: 521 helix: -0.26 (0.90), residues: 36 sheet: 0.50 (0.34), residues: 218 loop : -1.42 (0.37), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 161 HIS 0.002 0.001 HIS B 204 PHE 0.007 0.001 PHE A 153 TYR 0.012 0.001 TYR B 146 ARG 0.004 0.000 ARG A 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1817.61 seconds wall clock time: 32 minutes 49.78 seconds (1969.78 seconds total)