Starting phenix.real_space_refine on Tue Feb 11 03:20:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zan_39881/02_2025/8zan_39881.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zan_39881/02_2025/8zan_39881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zan_39881/02_2025/8zan_39881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zan_39881/02_2025/8zan_39881.map" model { file = "/net/cci-nas-00/data/ceres_data/8zan_39881/02_2025/8zan_39881.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zan_39881/02_2025/8zan_39881.cif" } resolution = 2.4 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= 0.007 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 34 5.16 5 C 2618 2.51 5 N 632 2.21 5 O 654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3938 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1949 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1949 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 7.79, per 1000 atoms: 1.98 Number of scatterers: 3938 At special positions: 0 Unit cell: (60.55, 72.45, 80.15, 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 34 16.00 O 654 8.00 N 632 7.00 C 2618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 34 " - pdb=" SG CYS B 36 " distance=2.03 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS B 34 " 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 480.1 milliseconds 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 884 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 82.1% 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 36 through 40 Processing helix chain 'A' and resid 47 through 77 Processing helix chain 'A' and resid 80 through 101 removed outlier: 3.900A pdb=" N ILE A 84 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU A 101 " --> pdb=" O GLU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 136 removed outlier: 3.575A pdb=" N TYR A 121 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Proline residue: A 129 - end of helix Processing helix chain 'A' and resid 146 through 168 Processing helix chain 'A' and resid 171 through 203 Processing helix chain 'A' and resid 206 through 233 Proline residue: A 227 - end of helix Processing helix chain 'A' and resid 240 through 257 Processing helix chain 'A' and resid 257 through 278 Processing helix chain 'B' and resid 36 through 40 Processing helix chain 'B' and resid 47 through 77 Processing helix chain 'B' and resid 80 through 101 removed outlier: 3.900A pdb=" N ILE B 84 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 136 removed outlier: 3.575A pdb=" N TYR B 121 " --> pdb=" O GLN B 117 " (cutoff:3.500A) Proline residue: B 129 - end of helix Processing helix chain 'B' and resid 146 through 168 Processing helix chain 'B' and resid 171 through 203 Processing helix chain 'B' and resid 206 through 233 Proline residue: B 227 - end of helix Processing helix chain 'B' and resid 240 through 257 Processing helix chain 'B' and resid 257 through 278 316 hydrogen bonds defined for protein. 936 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: 1.07 Time building geometry restraints manager: 1.28 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: 1164 1.34 - 1.46: 1178 1.46 - 1.58: 1668 1.58 - 1.70: 0 1.70 - 1.82: 50 Bond restraints: 4060 Sorted by residual: bond pdb=" C TYR B 35 " pdb=" O TYR B 35 " ideal model delta sigma weight residual 1.234 1.247 -0.013 8.30e-03 1.45e+04 2.40e+00 bond pdb=" C TYR A 35 " pdb=" O TYR A 35 " ideal model delta sigma weight residual 1.234 1.247 -0.012 8.30e-03 1.45e+04 2.22e+00 bond pdb=" N TYR A 35 " pdb=" CA TYR A 35 " ideal model delta sigma weight residual 1.468 1.454 0.014 1.24e-02 6.50e+03 1.30e+00 bond pdb=" N TYR B 35 " pdb=" CA TYR B 35 " ideal model delta sigma weight residual 1.468 1.454 0.014 1.24e-02 6.50e+03 1.29e+00 bond pdb=" C ASN B 104 " pdb=" N PRO B 105 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.28e+00 ... (remaining 4055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 5348 1.59 - 3.19: 148 3.19 - 4.78: 20 4.78 - 6.38: 4 6.38 - 7.97: 6 Bond angle restraints: 5526 Sorted by residual: angle pdb=" N SER B 106 " pdb=" CA SER B 106 " pdb=" C SER B 106 " ideal model delta sigma weight residual 114.62 108.55 6.07 1.14e+00 7.69e-01 2.83e+01 angle pdb=" N SER A 106 " pdb=" CA SER A 106 " pdb=" C SER A 106 " ideal model delta sigma weight residual 114.62 108.55 6.07 1.14e+00 7.69e-01 2.83e+01 angle pdb=" CA PRO A 105 " pdb=" N PRO A 105 " pdb=" CD PRO A 105 " ideal model delta sigma weight residual 112.00 106.01 5.99 1.40e+00 5.10e-01 1.83e+01 angle pdb=" CA PRO B 105 " pdb=" N PRO B 105 " pdb=" CD PRO B 105 " ideal model delta sigma weight residual 112.00 106.01 5.99 1.40e+00 5.10e-01 1.83e+01 angle pdb=" C ALA B 169 " pdb=" N THR B 170 " pdb=" CA THR B 170 " ideal model delta sigma weight residual 121.54 128.12 -6.58 1.91e+00 2.74e-01 1.19e+01 ... (remaining 5521 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.46: 1847 15.46 - 30.92: 286 30.92 - 46.38: 89 46.38 - 61.84: 24 61.84 - 77.30: 6 Dihedral angle restraints: 2252 sinusoidal: 852 harmonic: 1400 Sorted by residual: dihedral pdb=" CA ASN B 104 " pdb=" C ASN B 104 " pdb=" N PRO B 105 " pdb=" CA PRO B 105 " ideal model delta harmonic sigma weight residual -180.00 -151.91 -28.09 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA ASN A 104 " pdb=" C ASN A 104 " pdb=" N PRO A 105 " pdb=" CA PRO A 105 " ideal model delta harmonic sigma weight residual -180.00 -151.94 -28.06 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CB CYS A 36 " pdb=" SG CYS A 36 " pdb=" SG CYS B 34 " pdb=" CB CYS B 34 " ideal model delta sinusoidal sigma weight residual 93.00 59.82 33.18 1 1.00e+01 1.00e-02 1.57e+01 ... (remaining 2249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 487 0.049 - 0.097: 103 0.097 - 0.145: 10 0.145 - 0.194: 2 0.194 - 0.242: 2 Chirality restraints: 604 Sorted by residual: chirality pdb=" CA PRO A 105 " pdb=" N PRO A 105 " pdb=" C PRO A 105 " pdb=" CB PRO A 105 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA PRO B 105 " pdb=" N PRO B 105 " pdb=" C PRO B 105 " pdb=" CB PRO B 105 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA THR A 170 " pdb=" N THR A 170 " pdb=" C THR A 170 " pdb=" CB THR A 170 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.58e-01 ... (remaining 601 not shown) Planarity restraints: 668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 104 " 0.094 5.00e-02 4.00e+02 1.42e-01 3.23e+01 pdb=" N PRO B 105 " -0.246 5.00e-02 4.00e+02 pdb=" CA PRO B 105 " 0.078 5.00e-02 4.00e+02 pdb=" CD PRO B 105 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 104 " -0.094 5.00e-02 4.00e+02 1.42e-01 3.22e+01 pdb=" N PRO A 105 " 0.245 5.00e-02 4.00e+02 pdb=" CA PRO A 105 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO A 105 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 203 " -0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO A 204 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 204 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 204 " -0.017 5.00e-02 4.00e+02 ... (remaining 665 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1281 2.83 - 3.35: 3947 3.35 - 3.86: 7622 3.86 - 4.38: 8473 4.38 - 4.90: 13995 Nonbonded interactions: 35318 Sorted by model distance: nonbonded pdb=" O THR A 246 " pdb=" OG1 THR A 250 " model vdw 2.309 3.040 nonbonded pdb=" O THR B 246 " pdb=" OG1 THR B 250 " model vdw 2.309 3.040 nonbonded pdb=" O MET A 168 " pdb=" ND2 ASN B 104 " model vdw 2.345 3.120 nonbonded pdb=" ND2 ASN A 104 " pdb=" O MET B 168 " model vdw 2.345 3.120 nonbonded pdb=" O ASN B 46 " pdb=" ND2 ASN B 46 " model vdw 2.363 3.120 ... (remaining 35313 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' 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: 13.400 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: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 18.940 Find NCS groups from input model: 0.070 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:13.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4060 Z= 0.225 Angle : 0.650 7.970 5526 Z= 0.387 Chirality : 0.042 0.242 604 Planarity : 0.008 0.142 668 Dihedral : 17.049 77.298 1362 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 1.23 % Allowed : 5.33 % Favored : 93.44 % Rotamer: Outliers : 2.96 % Allowed : 19.70 % Favored : 77.34 % 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 (0.39), residues: 488 helix: 2.21 (0.26), residues: 372 sheet: None (None), residues: 0 loop : -2.36 (0.56), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 75 HIS 0.002 0.001 HIS B 114 PHE 0.010 0.002 PHE B 178 TYR 0.011 0.001 TYR A 109 ARG 0.002 0.000 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.450 Fit side-chains REVERT: A 56 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8245 (mt0) REVERT: A 93 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8075 (tmmm) REVERT: A 194 LYS cc_start: 0.8171 (mtpt) cc_final: 0.7770 (mmtt) REVERT: B 56 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8248 (mt0) REVERT: B 93 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8070 (tmmm) REVERT: B 194 LYS cc_start: 0.7928 (mmmt) cc_final: 0.7660 (mtpm) outliers start: 12 outliers final: 6 residues processed: 56 average time/residue: 1.3261 time to fit residues: 76.6920 Evaluate side-chains 56 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 276 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 46 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.124815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.109468 restraints weight = 4133.461| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.55 r_work: 0.3191 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.0696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4060 Z= 0.232 Angle : 0.605 8.179 5526 Z= 0.327 Chirality : 0.043 0.248 604 Planarity : 0.008 0.142 668 Dihedral : 7.262 53.344 574 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.82 % Allowed : 5.74 % Favored : 93.44 % Rotamer: Outliers : 1.48 % Allowed : 19.70 % Favored : 78.82 % 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: 1.83 (0.39), residues: 488 helix: 2.13 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -2.31 (0.58), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 75 HIS 0.002 0.001 HIS A 201 PHE 0.011 0.002 PHE B 178 TYR 0.014 0.001 TYR A 109 ARG 0.001 0.000 ARG B 209 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.418 Fit side-chains REVERT: A 103 LYS cc_start: 0.7507 (mmtm) cc_final: 0.6862 (mtpt) REVERT: A 194 LYS cc_start: 0.7728 (mtpt) cc_final: 0.6938 (mmtt) REVERT: B 103 LYS cc_start: 0.7509 (mmtm) cc_final: 0.6860 (mtpt) REVERT: B 194 LYS cc_start: 0.7422 (mmmt) cc_final: 0.6781 (mtpm) outliers start: 6 outliers final: 4 residues processed: 55 average time/residue: 1.3567 time to fit residues: 77.1879 Evaluate side-chains 55 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 147 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 46 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.124704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.109756 restraints weight = 4158.422| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.47 r_work: 0.3168 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4060 Z= 0.219 Angle : 0.589 8.243 5526 Z= 0.317 Chirality : 0.042 0.247 604 Planarity : 0.008 0.142 668 Dihedral : 6.371 53.788 554 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.82 % Allowed : 6.56 % Favored : 92.62 % Rotamer: Outliers : 2.46 % Allowed : 18.23 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 20.00 % 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: 1.89 (0.39), residues: 488 helix: 2.18 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -2.31 (0.58), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 118 HIS 0.002 0.001 HIS A 201 PHE 0.010 0.002 PHE A 178 TYR 0.014 0.001 TYR A 109 ARG 0.001 0.000 ARG B 268 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.401 Fit side-chains REVERT: A 103 LYS cc_start: 0.7186 (mmtm) cc_final: 0.6501 (mtpt) REVERT: A 194 LYS cc_start: 0.7413 (mtpt) cc_final: 0.6568 (mmtt) REVERT: A 273 GLU cc_start: 0.6700 (mt-10) cc_final: 0.6132 (tp30) REVERT: B 103 LYS cc_start: 0.7187 (mmtm) cc_final: 0.6500 (mtpt) REVERT: B 194 LYS cc_start: 0.7101 (mmmt) cc_final: 0.6412 (mtpm) REVERT: B 273 GLU cc_start: 0.6661 (mt-10) cc_final: 0.6103 (tp30) outliers start: 10 outliers final: 2 residues processed: 58 average time/residue: 1.3730 time to fit residues: 82.1589 Evaluate side-chains 56 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain B residue 139 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 43 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 47 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 46 ASN A 143 ASN B 46 ASN B 143 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.125473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.110503 restraints weight = 4125.660| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.47 r_work: 0.3178 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4060 Z= 0.203 Angle : 0.579 8.100 5526 Z= 0.310 Chirality : 0.042 0.248 604 Planarity : 0.008 0.141 668 Dihedral : 6.264 53.911 554 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.82 % Allowed : 6.56 % Favored : 92.62 % Rotamer: Outliers : 1.97 % Allowed : 19.21 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 20.00 % 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: 1.95 (0.39), residues: 488 helix: 2.23 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -2.34 (0.57), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 118 HIS 0.002 0.001 HIS B 201 PHE 0.010 0.002 PHE A 219 TYR 0.013 0.001 TYR A 109 ARG 0.001 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.385 Fit side-chains REVERT: A 103 LYS cc_start: 0.7142 (mmtm) cc_final: 0.6478 (mtpt) REVERT: A 194 LYS cc_start: 0.7383 (mtpt) cc_final: 0.6531 (mmtt) REVERT: A 273 GLU cc_start: 0.6693 (mt-10) cc_final: 0.6130 (tp30) REVERT: B 103 LYS cc_start: 0.7146 (mmtm) cc_final: 0.6478 (mtpt) REVERT: B 194 LYS cc_start: 0.7076 (mmmt) cc_final: 0.6386 (mtpm) REVERT: B 273 GLU cc_start: 0.6666 (mt-10) cc_final: 0.6107 (tp30) outliers start: 8 outliers final: 0 residues processed: 65 average time/residue: 1.2732 time to fit residues: 85.4937 Evaluate side-chains 56 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 104 ASN A 137 ASN B 46 ASN B 104 ASN B 137 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.124867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.109721 restraints weight = 4302.211| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.51 r_work: 0.3164 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4060 Z= 0.232 Angle : 0.593 8.283 5526 Z= 0.317 Chirality : 0.043 0.246 604 Planarity : 0.008 0.142 668 Dihedral : 6.084 52.089 552 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.97 % Favored : 92.62 % Rotamer: Outliers : 1.97 % Allowed : 18.72 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 20.00 % 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: 1.88 (0.39), residues: 488 helix: 2.24 (0.26), residues: 378 sheet: None (None), residues: 0 loop : -2.50 (0.56), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 118 HIS 0.002 0.001 HIS A 201 PHE 0.010 0.002 PHE B 178 TYR 0.013 0.001 TYR B 109 ARG 0.001 0.000 ARG B 268 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.348 Fit side-chains REVERT: A 56 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7616 (mt0) REVERT: A 103 LYS cc_start: 0.7209 (mmtm) cc_final: 0.6543 (mtpt) REVERT: A 194 LYS cc_start: 0.7427 (mtpt) cc_final: 0.6575 (mmtt) REVERT: A 273 GLU cc_start: 0.6726 (mt-10) cc_final: 0.6141 (tp30) REVERT: B 56 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7620 (mt0) REVERT: B 103 LYS cc_start: 0.7221 (mmtm) cc_final: 0.6547 (mtpt) REVERT: B 194 LYS cc_start: 0.7088 (mmmt) cc_final: 0.6391 (mtpm) REVERT: B 273 GLU cc_start: 0.6677 (mt-10) cc_final: 0.6109 (tp30) outliers start: 8 outliers final: 0 residues processed: 55 average time/residue: 1.5343 time to fit residues: 86.8502 Evaluate side-chains 55 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain B residue 56 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 34 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 104 ASN B 46 ASN B 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.124405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.109395 restraints weight = 4196.750| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.49 r_work: 0.3161 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4060 Z= 0.226 Angle : 0.600 9.341 5526 Z= 0.317 Chirality : 0.042 0.240 604 Planarity : 0.009 0.145 668 Dihedral : 6.129 52.107 552 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.97 % Favored : 92.62 % Rotamer: Outliers : 2.46 % Allowed : 18.23 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 20.00 % 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: 1.93 (0.39), residues: 488 helix: 2.24 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -2.42 (0.57), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 118 HIS 0.002 0.001 HIS A 201 PHE 0.010 0.002 PHE B 178 TYR 0.013 0.001 TYR A 109 ARG 0.001 0.000 ARG B 268 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.495 Fit side-chains REVERT: A 56 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7554 (mt0) REVERT: A 103 LYS cc_start: 0.7211 (mmtm) cc_final: 0.6569 (mtpt) REVERT: A 194 LYS cc_start: 0.7432 (mtpt) cc_final: 0.6573 (mmtt) REVERT: A 273 GLU cc_start: 0.6736 (mt-10) cc_final: 0.6140 (tp30) REVERT: B 56 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7561 (mt0) REVERT: B 103 LYS cc_start: 0.7224 (mmtm) cc_final: 0.6576 (mtpt) REVERT: B 194 LYS cc_start: 0.7093 (mmmt) cc_final: 0.6386 (mtpm) REVERT: B 273 GLU cc_start: 0.6697 (mt-10) cc_final: 0.6118 (tp30) outliers start: 10 outliers final: 4 residues processed: 56 average time/residue: 1.4204 time to fit residues: 82.0092 Evaluate side-chains 58 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 CYS Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 276 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 44 optimal weight: 0.0970 chunk 5 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 104 ASN B 46 ASN B 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.124690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.109639 restraints weight = 4198.490| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.50 r_work: 0.3166 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4060 Z= 0.210 Angle : 0.608 10.693 5526 Z= 0.318 Chirality : 0.041 0.229 604 Planarity : 0.009 0.150 668 Dihedral : 6.160 52.957 552 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.97 % Favored : 92.62 % Rotamer: Outliers : 2.46 % Allowed : 17.98 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 20.00 % 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: 1.97 (0.39), residues: 488 helix: 2.26 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -2.38 (0.57), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 118 HIS 0.002 0.001 HIS B 201 PHE 0.010 0.002 PHE B 178 TYR 0.013 0.001 TYR A 109 ARG 0.001 0.000 ARG B 268 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.404 Fit side-chains REVERT: A 56 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7552 (mt0) REVERT: A 103 LYS cc_start: 0.7216 (mmtm) cc_final: 0.6591 (mtpt) REVERT: A 194 LYS cc_start: 0.7407 (mtpt) cc_final: 0.6551 (mmtt) REVERT: A 273 GLU cc_start: 0.6708 (mt-10) cc_final: 0.6118 (tp30) REVERT: B 56 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7559 (mt0) REVERT: B 103 LYS cc_start: 0.7214 (mmtm) cc_final: 0.6586 (mtpt) REVERT: B 194 LYS cc_start: 0.7070 (mmmt) cc_final: 0.6361 (mtpm) REVERT: B 273 GLU cc_start: 0.6688 (mt-10) cc_final: 0.6107 (tp30) outliers start: 10 outliers final: 6 residues processed: 61 average time/residue: 1.3707 time to fit residues: 86.2583 Evaluate side-chains 61 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 CYS Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 276 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 46 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.124557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.109432 restraints weight = 4186.537| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.50 r_work: 0.3163 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4060 Z= 0.215 Angle : 0.614 11.201 5526 Z= 0.318 Chirality : 0.042 0.232 604 Planarity : 0.009 0.151 668 Dihedral : 6.151 52.462 552 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.97 % Favored : 92.62 % Rotamer: Outliers : 2.46 % Allowed : 18.72 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 20.00 % 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: 1.99 (0.39), residues: 488 helix: 2.28 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -2.37 (0.58), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 118 HIS 0.002 0.001 HIS B 201 PHE 0.010 0.002 PHE B 178 TYR 0.013 0.001 TYR A 109 ARG 0.001 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.459 Fit side-chains REVERT: A 56 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7551 (mt0) REVERT: A 103 LYS cc_start: 0.7265 (mmtm) cc_final: 0.6622 (mtpt) REVERT: A 194 LYS cc_start: 0.7402 (mtpt) cc_final: 0.6546 (mmtt) REVERT: A 273 GLU cc_start: 0.6720 (mt-10) cc_final: 0.6123 (tp30) REVERT: B 56 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7559 (mt0) REVERT: B 103 LYS cc_start: 0.7257 (mmtm) cc_final: 0.6601 (mtpt) REVERT: B 194 LYS cc_start: 0.7067 (mmmt) cc_final: 0.6356 (mtpm) REVERT: B 273 GLU cc_start: 0.6692 (mt-10) cc_final: 0.6109 (tp30) outliers start: 10 outliers final: 6 residues processed: 55 average time/residue: 1.3248 time to fit residues: 75.4858 Evaluate side-chains 59 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 CYS Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 276 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 27 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 chunk 44 optimal weight: 0.0000 chunk 17 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 46 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.124662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.109961 restraints weight = 4234.766| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.47 r_work: 0.3168 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4060 Z= 0.205 Angle : 0.613 11.347 5526 Z= 0.317 Chirality : 0.041 0.235 604 Planarity : 0.009 0.151 668 Dihedral : 6.139 53.359 552 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.97 % Favored : 92.62 % Rotamer: Outliers : 2.96 % Allowed : 18.23 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 20.00 % 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: 2.03 (0.39), residues: 488 helix: 2.29 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -2.31 (0.58), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 118 HIS 0.002 0.001 HIS B 201 PHE 0.010 0.002 PHE A 219 TYR 0.013 0.001 TYR A 109 ARG 0.001 0.000 ARG B 268 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.393 Fit side-chains REVERT: A 56 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7594 (mt0) REVERT: A 103 LYS cc_start: 0.7349 (mmtm) cc_final: 0.6698 (mtpt) REVERT: A 194 LYS cc_start: 0.7453 (mtpt) cc_final: 0.6606 (mmtt) REVERT: A 273 GLU cc_start: 0.6767 (mt-10) cc_final: 0.6183 (tp30) REVERT: B 56 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7602 (mt0) REVERT: B 103 LYS cc_start: 0.7354 (mmtm) cc_final: 0.6702 (mtpt) REVERT: B 194 LYS cc_start: 0.7122 (mmmt) cc_final: 0.6420 (mtpm) REVERT: B 273 GLU cc_start: 0.6748 (mt-10) cc_final: 0.6168 (tp30) outliers start: 12 outliers final: 8 residues processed: 59 average time/residue: 1.2824 time to fit residues: 78.3559 Evaluate side-chains 63 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 CYS Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 276 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 42 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 137 ASN B 46 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.124909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.110173 restraints weight = 4196.684| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.44 r_work: 0.3169 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4060 Z= 0.210 Angle : 0.619 11.507 5526 Z= 0.320 Chirality : 0.042 0.237 604 Planarity : 0.009 0.151 668 Dihedral : 6.116 52.863 552 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.97 % Favored : 92.62 % Rotamer: Outliers : 2.71 % Allowed : 17.98 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 20.00 % 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: 2.06 (0.39), residues: 488 helix: 2.31 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -2.30 (0.58), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 118 HIS 0.002 0.001 HIS B 201 PHE 0.010 0.002 PHE A 219 TYR 0.013 0.001 TYR A 109 ARG 0.001 0.000 ARG B 268 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.477 Fit side-chains REVERT: A 56 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7567 (mt0) REVERT: A 103 LYS cc_start: 0.7322 (mmtm) cc_final: 0.6662 (mtpt) REVERT: A 194 LYS cc_start: 0.7420 (mtpt) cc_final: 0.6574 (mmtt) REVERT: A 273 GLU cc_start: 0.6740 (mt-10) cc_final: 0.6157 (tp30) REVERT: B 56 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7579 (mt0) REVERT: B 103 LYS cc_start: 0.7329 (mmtm) cc_final: 0.6669 (mtpt) REVERT: B 194 LYS cc_start: 0.7086 (mmmt) cc_final: 0.6382 (mtpm) REVERT: B 273 GLU cc_start: 0.6726 (mt-10) cc_final: 0.6148 (tp30) outliers start: 11 outliers final: 7 residues processed: 59 average time/residue: 1.2521 time to fit residues: 76.4885 Evaluate side-chains 63 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 CYS Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 276 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 30 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 10 optimal weight: 0.1980 chunk 9 optimal weight: 0.3980 chunk 6 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 46 ASN B 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.125758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.111024 restraints weight = 4170.832| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.45 r_work: 0.3180 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4060 Z= 0.200 Angle : 0.617 11.516 5526 Z= 0.318 Chirality : 0.041 0.239 604 Planarity : 0.009 0.151 668 Dihedral : 6.083 53.487 552 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.97 % Favored : 92.62 % Rotamer: Outliers : 2.46 % Allowed : 18.23 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 20.00 % 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: 2.09 (0.39), residues: 488 helix: 2.33 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -2.28 (0.59), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 118 HIS 0.002 0.001 HIS B 201 PHE 0.010 0.002 PHE A 219 TYR 0.013 0.001 TYR A 109 ARG 0.000 0.000 ARG A 268 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4813.75 seconds wall clock time: 86 minutes 16.31 seconds (5176.31 seconds total)