Starting phenix.real_space_refine on Wed Mar 5 22:31:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zan_39881/03_2025/8zan_39881.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zan_39881/03_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_39881/03_2025/8zan_39881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zan_39881/03_2025/8zan_39881.map" model { file = "/net/cci-nas-00/data/ceres_data/8zan_39881/03_2025/8zan_39881.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zan_39881/03_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-5624/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: 7.10, per 1000 atoms: 1.80 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: 1.13 Conformation dependent library (CDL) restraints added in 478.0 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: 0.30 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: 1.08 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: 19.970 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: 0.350 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.240 Find NCS groups from input model: 0.060 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:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.060 ------------------------------------------------------------------------------- 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 : 0.408 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: 1.2576 time to fit residues: 72.8117 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 : 0.452 ------------------------------------------------------------------------------- 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 = 0.3487 r_free = 0.3487 target = 0.124756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.109584 restraints weight = 4141.151| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.54 r_work: 0.3193 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 : 0.438 Fit side-chains REVERT: A 103 LYS cc_start: 0.7516 (mmtm) cc_final: 0.6872 (mtpt) REVERT: A 194 LYS cc_start: 0.7734 (mtpt) cc_final: 0.6945 (mmtt) REVERT: B 103 LYS cc_start: 0.7517 (mmtm) cc_final: 0.6869 (mtpt) REVERT: B 194 LYS cc_start: 0.7429 (mmmt) cc_final: 0.6789 (mtpm) outliers start: 6 outliers final: 4 residues processed: 55 average time/residue: 1.4209 time to fit residues: 80.6893 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 : 0.428 ------------------------------------------------------------------------------- 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: 0.7980 chunk 8 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.124909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.109812 restraints weight = 4164.536| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.55 r_work: 0.3196 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.0806 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= 0.223 Angle : 0.591 8.299 5526 Z= 0.318 Chirality : 0.042 0.247 604 Planarity : 0.008 0.142 668 Dihedral : 6.376 53.571 554 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.66 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: 1.88 (0.39), residues: 488 helix: 2.17 (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 : 0.393 Fit side-chains REVERT: A 103 LYS cc_start: 0.7534 (mmtm) cc_final: 0.6892 (mtpt) REVERT: A 194 LYS cc_start: 0.7739 (mtpt) cc_final: 0.6941 (mmtt) REVERT: A 273 GLU cc_start: 0.6915 (mt-10) cc_final: 0.6341 (tp30) REVERT: B 103 LYS cc_start: 0.7524 (mmtm) cc_final: 0.6878 (mtpt) REVERT: B 194 LYS cc_start: 0.7439 (mmmt) cc_final: 0.6802 (mtpm) REVERT: B 273 GLU cc_start: 0.6871 (mt-10) cc_final: 0.6308 (tp30) outliers start: 10 outliers final: 2 residues processed: 58 average time/residue: 1.3211 time to fit residues: 79.1068 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 : 0.432 ------------------------------------------------------------------------------- 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: 0.6980 chunk 5 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.124039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.108992 restraints weight = 4127.676| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.47 r_work: 0.3160 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4060 Z= 0.228 Angle : 0.597 8.476 5526 Z= 0.319 Chirality : 0.042 0.247 604 Planarity : 0.008 0.142 668 Dihedral : 6.309 52.393 554 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.41 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: 1.88 (0.39), residues: 488 helix: 2.19 (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 0.011 0.002 PHE A 178 TYR 0.014 0.001 TYR A 109 ARG 0.001 0.000 ARG A 268 *********************** 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 68 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.438 Fit side-chains REVERT: A 103 LYS cc_start: 0.7161 (mmtm) cc_final: 0.6491 (mtpt) REVERT: A 194 LYS cc_start: 0.7398 (mtpt) cc_final: 0.6541 (mmtt) REVERT: A 273 GLU cc_start: 0.6700 (mt-10) cc_final: 0.6126 (tp30) REVERT: B 103 LYS cc_start: 0.7169 (mmtm) cc_final: 0.6496 (mtpt) REVERT: B 194 LYS cc_start: 0.7061 (mmmt) cc_final: 0.6364 (mtpm) REVERT: B 273 GLU cc_start: 0.6663 (mt-10) cc_final: 0.6098 (tp30) outliers start: 8 outliers final: 0 residues processed: 62 average time/residue: 1.3291 time to fit residues: 84.9718 Evaluate side-chains 54 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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: 0.7980 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 104 ASN B 46 ASN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.123880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.108741 restraints weight = 4298.247| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.51 r_work: 0.3152 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4060 Z= 0.248 Angle : 0.606 8.663 5526 Z= 0.323 Chirality : 0.043 0.245 604 Planarity : 0.008 0.143 668 Dihedral : 6.139 51.477 552 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.97 % Favored : 92.62 % Rotamer: Outliers : 1.72 % Allowed : 18.72 % 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: 1.84 (0.39), residues: 488 helix: 2.21 (0.26), residues: 378 sheet: None (None), residues: 0 loop : -2.52 (0.55), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 118 HIS 0.003 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 A 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: 7 poor density : 54 time to evaluate : 0.454 Fit side-chains REVERT: A 56 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7620 (mt0) REVERT: A 103 LYS cc_start: 0.7223 (mmtm) cc_final: 0.6552 (mtpt) REVERT: A 194 LYS cc_start: 0.7432 (mtpt) cc_final: 0.6575 (mmtt) REVERT: A 273 GLU cc_start: 0.6744 (mt-10) cc_final: 0.6148 (tp30) REVERT: B 56 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7624 (mt0) REVERT: B 103 LYS cc_start: 0.7232 (mmtm) cc_final: 0.6559 (mtpt) REVERT: B 194 LYS cc_start: 0.7083 (mmmt) cc_final: 0.6375 (mtpm) REVERT: B 273 GLU cc_start: 0.6701 (mt-10) cc_final: 0.6124 (tp30) outliers start: 7 outliers final: 2 residues processed: 55 average time/residue: 1.5217 time to fit residues: 86.2727 Evaluate side-chains 58 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 276 LEU 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: 1.9990 chunk 34 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.124040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.109009 restraints weight = 4190.012| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.49 r_work: 0.3157 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4060 Z= 0.230 Angle : 0.601 9.620 5526 Z= 0.319 Chirality : 0.042 0.245 604 Planarity : 0.009 0.146 668 Dihedral : 6.159 52.079 552 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.97 % Favored : 92.62 % Rotamer: Outliers : 2.71 % Allowed : 17.73 % 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: 1.90 (0.39), residues: 488 helix: 2.21 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -2.40 (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 0.011 0.002 PHE A 178 TYR 0.013 0.001 TYR A 109 ARG 0.001 0.000 ARG A 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 65 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.388 Fit side-chains REVERT: A 56 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7551 (mt0) REVERT: A 103 LYS cc_start: 0.7213 (mmtm) cc_final: 0.6570 (mtpt) REVERT: A 194 LYS cc_start: 0.7412 (mtpt) cc_final: 0.6550 (mmtt) REVERT: A 273 GLU cc_start: 0.6739 (mt-10) cc_final: 0.6141 (tp30) REVERT: B 56 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7553 (mt0) REVERT: B 103 LYS cc_start: 0.7228 (mmtm) cc_final: 0.6559 (mtpt) REVERT: B 194 LYS cc_start: 0.7072 (mmmt) cc_final: 0.6358 (mtpm) REVERT: B 273 GLU cc_start: 0.6703 (mt-10) cc_final: 0.6123 (tp30) outliers start: 11 outliers final: 6 residues processed: 59 average time/residue: 1.4046 time to fit residues: 85.4695 Evaluate side-chains 62 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 44 optimal weight: 0.0470 chunk 5 optimal weight: 1.9990 chunk 41 optimal weight: 0.0010 chunk 24 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.4284 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.127124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.112281 restraints weight = 4193.001| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.49 r_work: 0.3201 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4060 Z= 0.180 Angle : 0.575 10.380 5526 Z= 0.303 Chirality : 0.041 0.248 604 Planarity : 0.009 0.149 668 Dihedral : 6.110 54.753 552 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.97 % Favored : 92.62 % Rotamer: Outliers : 2.71 % Allowed : 17.49 % Favored : 79.80 % 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: 2.35 (0.26), residues: 378 sheet: None (None), residues: 0 loop : -2.35 (0.58), residues: 110 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 0.001 PHE A 219 TYR 0.012 0.001 TYR A 109 ARG 0.000 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 69 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.450 Fit side-chains REVERT: A 56 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7546 (mt0) REVERT: A 103 LYS cc_start: 0.7225 (mmtm) cc_final: 0.6624 (mtpt) REVERT: A 194 LYS cc_start: 0.7402 (mtpt) cc_final: 0.6541 (mmtt) REVERT: A 273 GLU cc_start: 0.6697 (mt-10) cc_final: 0.6126 (tp30) REVERT: B 56 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7542 (mt0) REVERT: B 103 LYS cc_start: 0.7226 (mmtm) cc_final: 0.6567 (mtpt) REVERT: B 194 LYS cc_start: 0.7072 (mmmt) cc_final: 0.6481 (mmtt) REVERT: B 273 GLU cc_start: 0.6679 (mt-10) cc_final: 0.6116 (tp30) outliers start: 11 outliers final: 4 residues processed: 63 average time/residue: 1.1507 time to fit residues: 75.1876 Evaluate side-chains 60 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 B residue 56 GLN Chi-restraints excluded: chain B residue 139 THR 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: 0.7980 chunk 39 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 B 137 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.124859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.109860 restraints weight = 4188.663| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.49 r_work: 0.3168 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4060 Z= 0.224 Angle : 0.606 11.294 5526 Z= 0.317 Chirality : 0.042 0.246 604 Planarity : 0.009 0.151 668 Dihedral : 6.064 51.217 552 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.97 % Favored : 92.62 % Rotamer: Outliers : 2.96 % Allowed : 16.75 % Favored : 80.30 % 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: 2.27 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -2.40 (0.58), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 118 HIS 0.003 0.001 HIS B 201 PHE 0.011 0.002 PHE B 178 TYR 0.014 0.001 TYR A 109 ARG 0.001 0.000 ARG A 268 *********************** 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 67 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.430 Fit side-chains REVERT: A 56 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7562 (mt0) REVERT: A 103 LYS cc_start: 0.7266 (mmtm) cc_final: 0.6631 (mtpt) REVERT: A 194 LYS cc_start: 0.7396 (mtpt) cc_final: 0.6551 (mmtt) REVERT: A 273 GLU cc_start: 0.6719 (mt-10) cc_final: 0.6126 (tp30) REVERT: B 56 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7565 (mt0) REVERT: B 103 LYS cc_start: 0.7224 (mmtm) cc_final: 0.6553 (mtpt) REVERT: B 194 LYS cc_start: 0.7082 (mmmt) cc_final: 0.6370 (mtpm) REVERT: B 273 GLU cc_start: 0.6695 (mt-10) cc_final: 0.6116 (tp30) outliers start: 12 outliers final: 8 residues processed: 61 average time/residue: 1.2661 time to fit residues: 79.9107 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 : 0.453 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 27 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 44 optimal weight: 0.0670 chunk 17 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 = 0.124643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.109770 restraints weight = 4223.593| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.46 r_work: 0.3163 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4060 Z= 0.218 Angle : 0.608 11.532 5526 Z= 0.317 Chirality : 0.042 0.247 604 Planarity : 0.009 0.151 668 Dihedral : 6.108 52.519 552 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.97 % Favored : 92.62 % Rotamer: Outliers : 2.96 % Allowed : 17.73 % 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: 2.02 (0.38), residues: 488 helix: 2.28 (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 178 TYR 0.013 0.001 TYR A 109 ARG 0.001 0.000 ARG B 147 *********************** 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 63 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.437 Fit side-chains REVERT: A 56 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7556 (mt0) REVERT: A 103 LYS cc_start: 0.7286 (mmtm) cc_final: 0.6630 (mtpt) REVERT: A 194 LYS cc_start: 0.7372 (mtpt) cc_final: 0.6528 (mmtt) REVERT: A 273 GLU cc_start: 0.6726 (mt-10) cc_final: 0.6137 (tp30) REVERT: B 56 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7552 (mt0) REVERT: B 103 LYS cc_start: 0.7223 (mmtm) cc_final: 0.6553 (mtpt) REVERT: B 194 LYS cc_start: 0.7068 (mmmt) cc_final: 0.6357 (mtpm) REVERT: B 273 GLU cc_start: 0.6705 (mt-10) cc_final: 0.6122 (tp30) outliers start: 12 outliers final: 8 residues processed: 57 average time/residue: 1.1690 time to fit residues: 69.1217 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 : 0.352 ------------------------------------------------------------------------------- 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: 1.9990 chunk 16 optimal weight: 0.7980 chunk 30 optimal weight: 0.0050 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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 = 0.3442 r_free = 0.3442 target = 0.123955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.109503 restraints weight = 4213.818| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.43 r_work: 0.3166 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4060 Z= 0.221 Angle : 0.611 11.780 5526 Z= 0.319 Chirality : 0.042 0.248 604 Planarity : 0.009 0.152 668 Dihedral : 6.109 52.399 552 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.97 % Favored : 92.62 % Rotamer: Outliers : 2.96 % Allowed : 17.73 % 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: 2.02 (0.38), residues: 488 helix: 2.29 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -2.32 (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 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 64 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.401 Fit side-chains REVERT: A 56 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7521 (mt0) REVERT: A 103 LYS cc_start: 0.7255 (mmtm) cc_final: 0.6589 (mtpt) REVERT: A 194 LYS cc_start: 0.7336 (mtpt) cc_final: 0.6489 (mmtt) REVERT: A 273 GLU cc_start: 0.6707 (mt-10) cc_final: 0.6120 (tp30) REVERT: B 56 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7518 (mt0) REVERT: B 103 LYS cc_start: 0.7187 (mmtm) cc_final: 0.6513 (mtpt) REVERT: B 194 LYS cc_start: 0.7026 (mmmt) cc_final: 0.6313 (mtpm) REVERT: B 273 GLU cc_start: 0.6686 (mt-10) cc_final: 0.6105 (tp30) outliers start: 12 outliers final: 8 residues processed: 58 average time/residue: 1.2299 time to fit residues: 73.9063 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 : 0.402 ------------------------------------------------------------------------------- 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 30 optimal weight: 0.2980 chunk 19 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 10 optimal weight: 0.0020 chunk 9 optimal weight: 0.0980 chunk 6 optimal weight: 0.9990 overall best weight: 0.3588 ------------------------------------------------------------------------------- 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 = 0.3495 r_free = 0.3495 target = 0.128208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.113550 restraints weight = 4176.783| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.45 r_work: 0.3214 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4060 Z= 0.179 Angle : 0.585 11.609 5526 Z= 0.305 Chirality : 0.041 0.251 604 Planarity : 0.009 0.152 668 Dihedral : 6.029 54.929 552 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.17 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: 2.19 (0.39), residues: 488 helix: 2.40 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -2.23 (0.60), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 118 HIS 0.002 0.000 HIS B 201 PHE 0.010 0.001 PHE A 219 TYR 0.011 0.001 TYR A 109 ARG 0.000 0.000 ARG B 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4916.74 seconds wall clock time: 84 minutes 28.60 seconds (5068.60 seconds total)