Starting phenix.real_space_refine on Tue Feb 11 05:10:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sk0_25168/02_2025/7sk0_25168.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sk0_25168/02_2025/7sk0_25168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sk0_25168/02_2025/7sk0_25168.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sk0_25168/02_2025/7sk0_25168.map" model { file = "/net/cci-nas-00/data/ceres_data/7sk0_25168/02_2025/7sk0_25168.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sk0_25168/02_2025/7sk0_25168.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.264 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: 5 Type Number sf(0) Gaussians K 5 8.98 5 S 16 5.16 5 C 2781 2.51 5 N 654 2.21 5 O 712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4168 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2074 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 7, 'TRANS': 249} Chain: "B" Number of atoms: 2073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2073 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 7, 'TRANS': 249} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 13 Unusual residues: {' K': 5, 'OCT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'OCT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.16, per 1000 atoms: 0.76 Number of scatterers: 4168 At special positions: 0 Unit cell: (69.357, 69.357, 90.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 5 19.00 S 16 16.00 O 712 8.00 N 654 7.00 C 2781 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS B 69 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 860.2 milliseconds 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 952 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 83.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 24 through 67 removed outlier: 4.087A pdb=" N LEU A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) Proline residue: A 47 - end of helix Processing helix chain 'A' and resid 71 through 89 Processing helix chain 'A' and resid 103 through 116 Processing helix chain 'A' and resid 127 through 161 removed outlier: 3.528A pdb=" N ILE A 140 " --> pdb=" O ILE A 136 " (cutoff:3.500A) Proline residue: A 143 - end of helix removed outlier: 3.592A pdb=" N VAL A 158 " --> pdb=" O GLN A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 173 removed outlier: 3.755A pdb=" N VAL A 165 " --> pdb=" O THR A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 196 removed outlier: 3.543A pdb=" N ALA A 180 " --> pdb=" O LYS A 176 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE A 181 " --> pdb=" O GLN A 177 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL A 185 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 207 Processing helix chain 'A' and resid 211 through 225 removed outlier: 3.771A pdb=" N SER A 215 " --> pdb=" O ASN A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 270 Processing helix chain 'A' and resid 270 through 280 Processing helix chain 'B' and resid 25 through 67 removed outlier: 4.087A pdb=" N LEU B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) Proline residue: B 47 - end of helix Processing helix chain 'B' and resid 71 through 89 Processing helix chain 'B' and resid 103 through 116 Processing helix chain 'B' and resid 127 through 161 removed outlier: 3.529A pdb=" N ILE B 140 " --> pdb=" O ILE B 136 " (cutoff:3.500A) Proline residue: B 143 - end of helix removed outlier: 3.592A pdb=" N VAL B 158 " --> pdb=" O GLN B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 173 removed outlier: 3.754A pdb=" N VAL B 165 " --> pdb=" O THR B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 196 removed outlier: 3.542A pdb=" N ALA B 180 " --> pdb=" O LYS B 176 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE B 181 " --> pdb=" O GLN B 177 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL B 185 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU B 186 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 207 Processing helix chain 'B' and resid 211 through 225 removed outlier: 3.770A pdb=" N SER B 215 " --> pdb=" O ASN B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 270 Processing helix chain 'B' and resid 270 through 280 315 hydrogen bonds defined for protein. 945 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: 1.13 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1250 1.34 - 1.46: 1152 1.46 - 1.58: 1854 1.58 - 1.70: 0 1.70 - 1.82: 20 Bond restraints: 4276 Sorted by residual: bond pdb=" CG LEU B 79 " pdb=" CD1 LEU B 79 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.34e+00 bond pdb=" CG LEU A 79 " pdb=" CD1 LEU A 79 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.30e+00 bond pdb=" CG1 ILE A 258 " pdb=" CD1 ILE A 258 " ideal model delta sigma weight residual 1.513 1.433 0.080 3.90e-02 6.57e+02 4.25e+00 bond pdb=" CG1 ILE B 258 " pdb=" CD1 ILE B 258 " ideal model delta sigma weight residual 1.513 1.434 0.079 3.90e-02 6.57e+02 4.14e+00 bond pdb=" CB GLU A 207 " pdb=" CG GLU A 207 " ideal model delta sigma weight residual 1.520 1.463 0.057 3.00e-02 1.11e+03 3.64e+00 ... (remaining 4271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 5205 1.62 - 3.24: 472 3.24 - 4.86: 98 4.86 - 6.47: 22 6.47 - 8.09: 2 Bond angle restraints: 5799 Sorted by residual: angle pdb=" N ASP B 103 " pdb=" CA ASP B 103 " pdb=" C ASP B 103 " ideal model delta sigma weight residual 109.24 103.89 5.35 1.51e+00 4.39e-01 1.26e+01 angle pdb=" N ASP A 103 " pdb=" CA ASP A 103 " pdb=" C ASP A 103 " ideal model delta sigma weight residual 109.24 103.91 5.33 1.51e+00 4.39e-01 1.25e+01 angle pdb=" C ASN A 95 " pdb=" N ALA A 96 " pdb=" CA ALA A 96 " ideal model delta sigma weight residual 121.54 128.01 -6.47 1.91e+00 2.74e-01 1.15e+01 angle pdb=" C ASN B 95 " pdb=" N ALA B 96 " pdb=" CA ALA B 96 " ideal model delta sigma weight residual 121.54 127.98 -6.44 1.91e+00 2.74e-01 1.14e+01 angle pdb=" C TRP A 100 " pdb=" N ASN A 101 " pdb=" CA ASN A 101 " ideal model delta sigma weight residual 120.38 124.45 -4.07 1.37e+00 5.33e-01 8.84e+00 ... (remaining 5794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.79: 2155 15.79 - 31.57: 222 31.57 - 47.36: 40 47.36 - 63.15: 14 63.15 - 78.94: 8 Dihedral angle restraints: 2439 sinusoidal: 951 harmonic: 1488 Sorted by residual: dihedral pdb=" N ASN B 87 " pdb=" CA ASN B 87 " pdb=" CB ASN B 87 " pdb=" CG ASN B 87 " ideal model delta sinusoidal sigma weight residual -60.00 -113.65 53.65 3 1.50e+01 4.44e-03 9.22e+00 dihedral pdb=" N ASN A 87 " pdb=" CA ASN A 87 " pdb=" CB ASN A 87 " pdb=" CG ASN A 87 " ideal model delta sinusoidal sigma weight residual -60.00 -113.62 53.62 3 1.50e+01 4.44e-03 9.22e+00 dihedral pdb=" CB MET A 279 " pdb=" CG MET A 279 " pdb=" SD MET A 279 " pdb=" CE MET A 279 " ideal model delta sinusoidal sigma weight residual -180.00 -127.29 -52.71 3 1.50e+01 4.44e-03 9.14e+00 ... (remaining 2436 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 378 0.039 - 0.078: 160 0.078 - 0.117: 86 0.117 - 0.156: 22 0.156 - 0.194: 12 Chirality restraints: 658 Sorted by residual: chirality pdb=" CB VAL A 92 " pdb=" CA VAL A 92 " pdb=" CG1 VAL A 92 " pdb=" CG2 VAL A 92 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.45e-01 chirality pdb=" CG LEU A 254 " pdb=" CB LEU A 254 " pdb=" CD1 LEU A 254 " pdb=" CD2 LEU A 254 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.44e-01 chirality pdb=" CG LEU B 254 " pdb=" CB LEU B 254 " pdb=" CD1 LEU B 254 " pdb=" CD2 LEU B 254 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.24e-01 ... (remaining 655 not shown) Planarity restraints: 712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 254 " 0.022 2.00e-02 2.50e+03 4.43e-02 1.96e+01 pdb=" C LEU A 254 " -0.077 2.00e-02 2.50e+03 pdb=" O LEU A 254 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU A 255 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 254 " -0.022 2.00e-02 2.50e+03 4.41e-02 1.95e+01 pdb=" C LEU B 254 " 0.076 2.00e-02 2.50e+03 pdb=" O LEU B 254 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU B 255 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 80 " 0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C GLY A 80 " -0.057 2.00e-02 2.50e+03 pdb=" O GLY A 80 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG A 81 " 0.019 2.00e-02 2.50e+03 ... (remaining 709 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.63: 38 2.63 - 3.26: 4786 3.26 - 3.89: 8391 3.89 - 4.51: 11197 4.51 - 5.14: 16862 Nonbonded interactions: 41274 Sorted by model distance: nonbonded pdb=" OG SER B 71 " pdb=" OE1 GLN B 74 " model vdw 2.005 3.040 nonbonded pdb=" OG SER A 71 " pdb=" OE1 GLN A 74 " model vdw 2.005 3.040 nonbonded pdb=" ND2 ASN A 87 " pdb=" O GLY B 229 " model vdw 2.141 3.120 nonbonded pdb=" O GLY A 229 " pdb=" ND2 ASN B 87 " model vdw 2.230 3.120 nonbonded pdb=" O SER B 116 " pdb=" OG1 THR B 117 " model vdw 2.270 3.040 ... (remaining 41269 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 24 through 279 or (resid 280 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2)) or resid 401)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.390 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 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 : 0.009 0.080 4276 Z= 0.543 Angle : 1.042 8.092 5799 Z= 0.587 Chirality : 0.058 0.194 658 Planarity : 0.008 0.044 712 Dihedral : 14.222 78.936 1484 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.44 % Allowed : 1.33 % Favored : 98.23 % 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: 0.35 (0.36), residues: 510 helix: 0.73 (0.24), residues: 396 sheet: None (None), residues: 0 loop : -1.30 (0.65), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 100 HIS 0.013 0.003 HIS A 122 PHE 0.039 0.004 PHE B 144 TYR 0.031 0.005 TYR A 237 ARG 0.013 0.002 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 74 GLN cc_start: 0.7034 (mp10) cc_final: 0.6579 (mp10) REVERT: B 28 LEU cc_start: 0.8157 (mt) cc_final: 0.7842 (mt) REVERT: B 74 GLN cc_start: 0.7280 (mp10) cc_final: 0.6809 (mp10) REVERT: B 87 ASN cc_start: 0.7164 (OUTLIER) cc_final: 0.6932 (t0) REVERT: B 243 GLU cc_start: 0.7398 (mp0) cc_final: 0.7169 (mp0) outliers start: 2 outliers final: 0 residues processed: 101 average time/residue: 0.1129 time to fit residues: 15.4980 Evaluate side-chains 87 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN B 77 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.220508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.173880 restraints weight = 5250.824| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 2.65 r_work: 0.3924 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4276 Z= 0.242 Angle : 0.675 5.831 5799 Z= 0.369 Chirality : 0.044 0.184 658 Planarity : 0.005 0.026 712 Dihedral : 4.868 22.494 570 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.43 % Allowed : 6.86 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.39), residues: 510 helix: 1.81 (0.25), residues: 406 sheet: None (None), residues: 0 loop : -0.62 (0.78), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 210 HIS 0.003 0.001 HIS B 122 PHE 0.017 0.002 PHE B 133 TYR 0.014 0.002 TYR A 88 ARG 0.002 0.001 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 GLN cc_start: 0.7404 (mp10) cc_final: 0.6950 (mp10) REVERT: A 189 PHE cc_start: 0.5700 (m-10) cc_final: 0.5448 (m-10) REVERT: A 243 GLU cc_start: 0.7509 (mp0) cc_final: 0.7133 (mp0) REVERT: A 260 MET cc_start: 0.7612 (mmm) cc_final: 0.7387 (mmt) REVERT: A 276 PHE cc_start: 0.6637 (t80) cc_final: 0.6360 (t80) REVERT: B 28 LEU cc_start: 0.8205 (mt) cc_final: 0.7904 (mt) REVERT: B 49 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7377 (tm-30) REVERT: B 74 GLN cc_start: 0.7385 (mp10) cc_final: 0.6868 (mp10) REVERT: B 189 PHE cc_start: 0.5702 (m-10) cc_final: 0.5361 (m-10) REVERT: B 260 MET cc_start: 0.7623 (mmm) cc_final: 0.7419 (mmt) outliers start: 11 outliers final: 9 residues processed: 105 average time/residue: 0.1087 time to fit residues: 15.6709 Evaluate side-chains 105 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 232 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 13 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 21 optimal weight: 0.0070 chunk 19 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.223065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.176104 restraints weight = 5187.242| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 2.66 r_work: 0.3943 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4276 Z= 0.196 Angle : 0.606 7.238 5799 Z= 0.323 Chirality : 0.042 0.180 658 Planarity : 0.004 0.032 712 Dihedral : 4.677 18.881 568 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.21 % Allowed : 8.19 % Favored : 89.60 % 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: 2.33 (0.40), residues: 510 helix: 2.06 (0.25), residues: 410 sheet: None (None), residues: 0 loop : -0.63 (0.83), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 100 HIS 0.004 0.001 HIS B 67 PHE 0.014 0.002 PHE A 174 TYR 0.011 0.001 TYR A 88 ARG 0.003 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 74 GLN cc_start: 0.7355 (mp10) cc_final: 0.6644 (mp10) REVERT: A 243 GLU cc_start: 0.7558 (mp0) cc_final: 0.7131 (mp0) REVERT: B 28 LEU cc_start: 0.8160 (mt) cc_final: 0.7839 (mt) REVERT: B 74 GLN cc_start: 0.7408 (mp10) cc_final: 0.6675 (mp10) REVERT: B 196 PHE cc_start: 0.7122 (m-80) cc_final: 0.6726 (m-80) REVERT: B 243 GLU cc_start: 0.7641 (mp0) cc_final: 0.7249 (mp0) REVERT: B 279 MET cc_start: 0.4026 (ttt) cc_final: 0.3782 (ttp) outliers start: 10 outliers final: 9 residues processed: 103 average time/residue: 0.0988 time to fit residues: 14.4950 Evaluate side-chains 103 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 237 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 47 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 chunk 18 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 1 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN B 77 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.220291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.172701 restraints weight = 5295.906| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 2.71 r_work: 0.3906 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4276 Z= 0.216 Angle : 0.578 5.831 5799 Z= 0.316 Chirality : 0.041 0.200 658 Planarity : 0.004 0.034 712 Dihedral : 4.644 20.923 568 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.65 % Allowed : 10.18 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.41 (0.39), residues: 510 helix: 2.09 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -0.52 (0.84), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 100 HIS 0.002 0.000 HIS B 122 PHE 0.014 0.002 PHE A 174 TYR 0.010 0.001 TYR A 252 ARG 0.002 0.000 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8592 (tp) cc_final: 0.8279 (mm) REVERT: A 56 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7435 (tt) REVERT: A 74 GLN cc_start: 0.7352 (mp10) cc_final: 0.6681 (mp10) REVERT: A 231 TYR cc_start: 0.6399 (m-80) cc_final: 0.6145 (m-80) REVERT: A 243 GLU cc_start: 0.7522 (mp0) cc_final: 0.7079 (mp0) REVERT: B 56 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7312 (tt) REVERT: B 74 GLN cc_start: 0.7422 (mp10) cc_final: 0.6715 (mp10) REVERT: B 196 PHE cc_start: 0.7135 (m-80) cc_final: 0.6767 (m-80) REVERT: B 231 TYR cc_start: 0.6501 (m-80) cc_final: 0.6134 (m-80) REVERT: B 260 MET cc_start: 0.7724 (mmm) cc_final: 0.7446 (mmm) outliers start: 12 outliers final: 8 residues processed: 99 average time/residue: 0.1026 time to fit residues: 14.3424 Evaluate side-chains 104 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 237 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 41 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.218980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.171206 restraints weight = 5422.758| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 2.74 r_work: 0.3887 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4276 Z= 0.227 Angle : 0.581 5.862 5799 Z= 0.318 Chirality : 0.042 0.187 658 Planarity : 0.004 0.034 712 Dihedral : 4.611 22.568 568 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.21 % Allowed : 12.39 % Favored : 85.40 % 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: 2.45 (0.39), residues: 510 helix: 2.11 (0.25), residues: 414 sheet: None (None), residues: 0 loop : -0.51 (0.83), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 100 HIS 0.002 0.000 HIS B 122 PHE 0.014 0.002 PHE A 174 TYR 0.010 0.001 TYR B 137 ARG 0.002 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8542 (tp) cc_final: 0.8249 (mm) REVERT: A 56 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7264 (tt) REVERT: A 74 GLN cc_start: 0.7332 (mp10) cc_final: 0.6622 (mp10) REVERT: A 231 TYR cc_start: 0.6427 (m-80) cc_final: 0.5916 (m-80) REVERT: A 243 GLU cc_start: 0.7554 (mp0) cc_final: 0.7105 (mp0) REVERT: B 31 LEU cc_start: 0.8570 (tp) cc_final: 0.8292 (mm) REVERT: B 56 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7290 (tt) REVERT: B 74 GLN cc_start: 0.7398 (mp10) cc_final: 0.6659 (mp10) REVERT: B 231 TYR cc_start: 0.6499 (m-80) cc_final: 0.6011 (m-80) outliers start: 10 outliers final: 6 residues processed: 97 average time/residue: 0.1026 time to fit residues: 14.0455 Evaluate side-chains 99 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 237 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 1 optimal weight: 0.0980 chunk 16 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 2 optimal weight: 0.0010 chunk 9 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.222631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.175407 restraints weight = 5319.192| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 2.73 r_work: 0.3930 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4276 Z= 0.189 Angle : 0.574 8.932 5799 Z= 0.312 Chirality : 0.040 0.162 658 Planarity : 0.004 0.036 712 Dihedral : 4.466 21.137 568 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.77 % Allowed : 13.05 % Favored : 85.18 % 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: 2.64 (0.39), residues: 510 helix: 2.25 (0.25), residues: 414 sheet: None (None), residues: 0 loop : -0.49 (0.81), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 100 HIS 0.002 0.000 HIS B 67 PHE 0.014 0.001 PHE B 174 TYR 0.008 0.001 TYR B 137 ARG 0.001 0.000 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8453 (tp) cc_final: 0.8186 (mm) REVERT: A 56 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7289 (tp) REVERT: A 74 GLN cc_start: 0.7304 (mp10) cc_final: 0.6573 (mp10) REVERT: A 231 TYR cc_start: 0.6346 (m-80) cc_final: 0.5883 (m-80) REVERT: B 31 LEU cc_start: 0.8532 (tp) cc_final: 0.8283 (mm) REVERT: B 56 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7297 (tt) REVERT: B 74 GLN cc_start: 0.7335 (mp10) cc_final: 0.6723 (mp10) REVERT: B 196 PHE cc_start: 0.6976 (m-80) cc_final: 0.6613 (m-80) REVERT: B 223 LEU cc_start: 0.9023 (mp) cc_final: 0.8774 (mt) REVERT: B 231 TYR cc_start: 0.6540 (m-80) cc_final: 0.6101 (m-80) REVERT: B 243 GLU cc_start: 0.7562 (mp0) cc_final: 0.7088 (mp0) REVERT: B 260 MET cc_start: 0.7833 (mmm) cc_final: 0.7626 (mmm) outliers start: 8 outliers final: 5 residues processed: 100 average time/residue: 0.0969 time to fit residues: 13.8064 Evaluate side-chains 100 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 237 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 35 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.218712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.170880 restraints weight = 5313.188| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 2.72 r_work: 0.3883 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 4276 Z= 0.246 Angle : 0.603 5.977 5799 Z= 0.332 Chirality : 0.042 0.204 658 Planarity : 0.004 0.034 712 Dihedral : 4.518 22.451 568 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.77 % Allowed : 14.60 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.39), residues: 510 helix: 2.07 (0.25), residues: 414 sheet: None (None), residues: 0 loop : -0.61 (0.81), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 100 HIS 0.004 0.000 HIS B 122 PHE 0.014 0.002 PHE A 144 TYR 0.013 0.001 TYR A 137 ARG 0.002 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8443 (tp) cc_final: 0.8204 (mm) REVERT: A 56 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7272 (tt) REVERT: A 74 GLN cc_start: 0.7355 (mp10) cc_final: 0.6627 (mp10) REVERT: A 231 TYR cc_start: 0.6418 (m-80) cc_final: 0.5777 (m-80) REVERT: A 243 GLU cc_start: 0.7551 (mp0) cc_final: 0.7082 (mp0) REVERT: B 31 LEU cc_start: 0.8577 (tp) cc_final: 0.8262 (mm) REVERT: B 56 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7064 (tt) REVERT: B 74 GLN cc_start: 0.7413 (mp10) cc_final: 0.6715 (mp10) REVERT: B 196 PHE cc_start: 0.7055 (m-80) cc_final: 0.6823 (m-80) REVERT: B 231 TYR cc_start: 0.6493 (m-80) cc_final: 0.5896 (m-80) REVERT: B 243 GLU cc_start: 0.7602 (mp0) cc_final: 0.7134 (mp0) outliers start: 8 outliers final: 5 residues processed: 100 average time/residue: 0.1000 time to fit residues: 14.2608 Evaluate side-chains 105 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 237 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.218126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.170313 restraints weight = 5342.659| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 2.68 r_work: 0.3884 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 4276 Z= 0.266 Angle : 0.646 10.148 5799 Z= 0.348 Chirality : 0.044 0.243 658 Planarity : 0.004 0.035 712 Dihedral : 4.537 22.518 568 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.21 % Allowed : 15.04 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.22 (0.39), residues: 510 helix: 1.98 (0.25), residues: 414 sheet: None (None), residues: 0 loop : -0.73 (0.81), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 210 HIS 0.002 0.000 HIS B 122 PHE 0.013 0.002 PHE A 174 TYR 0.016 0.002 TYR A 30 ARG 0.001 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7252 (tt) REVERT: A 74 GLN cc_start: 0.7362 (mp10) cc_final: 0.6652 (mp10) REVERT: A 231 TYR cc_start: 0.6491 (m-80) cc_final: 0.5846 (m-80) REVERT: B 31 LEU cc_start: 0.8608 (tp) cc_final: 0.8302 (mm) REVERT: B 56 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7165 (tt) REVERT: B 74 GLN cc_start: 0.7448 (mp10) cc_final: 0.6785 (mp10) REVERT: B 231 TYR cc_start: 0.6575 (m-80) cc_final: 0.5993 (m-80) REVERT: B 260 MET cc_start: 0.8057 (mmm) cc_final: 0.7836 (mmm) outliers start: 10 outliers final: 7 residues processed: 101 average time/residue: 0.0979 time to fit residues: 13.9914 Evaluate side-chains 107 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 237 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.218162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.170261 restraints weight = 5322.449| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 2.71 r_work: 0.3886 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 4276 Z= 0.271 Angle : 0.686 11.143 5799 Z= 0.358 Chirality : 0.044 0.260 658 Planarity : 0.004 0.035 712 Dihedral : 4.510 22.404 568 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.43 % Allowed : 15.04 % Favored : 82.52 % 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: 2.15 (0.39), residues: 510 helix: 1.98 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -1.00 (0.79), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 210 HIS 0.002 0.000 HIS B 122 PHE 0.013 0.002 PHE A 174 TYR 0.017 0.002 TYR B 30 ARG 0.002 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7350 (tt) REVERT: A 74 GLN cc_start: 0.7460 (mp10) cc_final: 0.6711 (mp10) REVERT: A 231 TYR cc_start: 0.6497 (m-80) cc_final: 0.5818 (m-80) REVERT: B 56 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7130 (tt) REVERT: B 74 GLN cc_start: 0.7543 (mp10) cc_final: 0.6850 (mp10) REVERT: B 231 TYR cc_start: 0.6578 (m-80) cc_final: 0.6032 (m-80) REVERT: B 260 MET cc_start: 0.8074 (mmm) cc_final: 0.7825 (mmm) outliers start: 11 outliers final: 8 residues processed: 102 average time/residue: 0.1020 time to fit residues: 14.6382 Evaluate side-chains 106 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 237 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 9 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 39 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 41 optimal weight: 0.1980 chunk 12 optimal weight: 0.5980 chunk 38 optimal weight: 0.0050 chunk 49 optimal weight: 0.3980 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.223653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.176357 restraints weight = 5363.174| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 2.78 r_work: 0.3942 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 4276 Z= 0.212 Angle : 0.662 12.669 5799 Z= 0.344 Chirality : 0.042 0.220 658 Planarity : 0.004 0.036 712 Dihedral : 4.311 21.433 568 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.88 % Allowed : 16.59 % Favored : 82.52 % 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: 2.42 (0.39), residues: 510 helix: 2.19 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -0.99 (0.76), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 100 HIS 0.003 0.000 HIS B 122 PHE 0.014 0.001 PHE B 133 TYR 0.016 0.001 TYR B 30 ARG 0.001 0.000 ARG B 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7336 (tt) REVERT: A 74 GLN cc_start: 0.7428 (mp10) cc_final: 0.6673 (mp10) REVERT: A 231 TYR cc_start: 0.6376 (m-80) cc_final: 0.5975 (m-80) REVERT: A 243 GLU cc_start: 0.7553 (mp0) cc_final: 0.7109 (mp0) REVERT: B 31 LEU cc_start: 0.8488 (tp) cc_final: 0.8217 (mm) REVERT: B 56 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7351 (tt) REVERT: B 243 GLU cc_start: 0.7520 (mp0) cc_final: 0.7091 (mp0) outliers start: 4 outliers final: 2 residues processed: 95 average time/residue: 0.0956 time to fit residues: 13.0299 Evaluate side-chains 93 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 237 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 32 optimal weight: 0.0470 chunk 44 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 1 optimal weight: 0.3980 chunk 19 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.222030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.175483 restraints weight = 5245.053| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 2.68 r_work: 0.3929 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 4276 Z= 0.228 Angle : 0.680 12.352 5799 Z= 0.351 Chirality : 0.042 0.221 658 Planarity : 0.004 0.036 712 Dihedral : 4.302 21.566 568 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.66 % Allowed : 17.48 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.30 (0.39), residues: 510 helix: 2.07 (0.25), residues: 414 sheet: None (None), residues: 0 loop : -0.92 (0.77), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 210 HIS 0.003 0.000 HIS B 122 PHE 0.013 0.001 PHE B 133 TYR 0.016 0.001 TYR B 30 ARG 0.001 0.000 ARG A 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2109.99 seconds wall clock time: 38 minutes 17.18 seconds (2297.18 seconds total)