Starting phenix.real_space_refine on Wed Jun 4 18:58:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zan_39881/06_2025/8zan_39881.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zan_39881/06_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_39881/06_2025/8zan_39881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zan_39881/06_2025/8zan_39881.map" model { file = "/net/cci-nas-00/data/ceres_data/8zan_39881/06_2025/8zan_39881.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zan_39881/06_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-5710/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: 9.07, per 1000 atoms: 2.30 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: 0.93 Conformation dependent library (CDL) restraints added in 400.3 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: 0.34 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: 1.11 Time building geometry restraints manager: 1.08 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: 26.770 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: 0.390 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 19.560 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:15.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.910 ------------------------------------------------------------------------------- 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 4066 Z= 0.171 Angle : 0.651 7.970 5530 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 Details of bonding type rmsd hydrogen bonds : bond 0.11505 ( 316) hydrogen bonds : angle 5.26418 ( 936) SS BOND : bond 0.00297 ( 2) SS BOND : angle 1.04719 ( 4) covalent geometry : bond 0.00346 ( 4060) covalent geometry : angle 0.65013 ( 5526) Misc. bond : bond 0.00192 ( 4) *********************** 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 : 0.399 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: 1.3314 time to fit residues: 77.0403 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 : 0.432 ------------------------------------------------------------------------------- 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: 0.8980 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3480 r_free = 0.3480 target = 0.124040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.108686 restraints weight = 4140.512| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.55 r_work: 0.3185 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.0711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4066 Z= 0.178 Angle : 0.616 8.367 5530 Z= 0.333 Chirality : 0.043 0.249 604 Planarity : 0.009 0.143 668 Dihedral : 7.293 52.435 574 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.82 % Allowed : 5.33 % Favored : 93.85 % 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 : 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: 1.79 (0.39), residues: 488 helix: 2.10 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -2.33 (0.57), 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 0.015 0.001 TYR A 109 ARG 0.001 0.000 ARG B 209 Details of bonding type rmsd hydrogen bonds : bond 0.04669 ( 316) hydrogen bonds : angle 4.78724 ( 936) SS BOND : bond 0.00135 ( 2) SS BOND : angle 0.52039 ( 4) covalent geometry : bond 0.00386 ( 4060) covalent geometry : angle 0.61598 ( 5526) Misc. bond : bond 0.00185 ( 4) *********************** 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 61 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.444 Fit side-chains REVERT: A 103 LYS cc_start: 0.7534 (mmtm) cc_final: 0.6857 (mtpt) REVERT: A 194 LYS cc_start: 0.7743 (mtpt) cc_final: 0.6949 (mmtt) REVERT: A 273 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6351 (tp30) REVERT: B 103 LYS cc_start: 0.7524 (mmtm) cc_final: 0.6841 (mtpt) REVERT: B 194 LYS cc_start: 0.7429 (mmmt) cc_final: 0.6780 (mtpm) REVERT: B 273 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6329 (tp30) outliers start: 6 outliers final: 4 residues processed: 57 average time/residue: 1.4751 time to fit residues: 86.5747 Evaluate side-chains 57 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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: 0.6980 chunk 21 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3453 r_free = 0.3453 target = 0.124273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.109322 restraints weight = 4155.716| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.47 r_work: 0.3163 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4066 Z= 0.165 Angle : 0.594 8.421 5530 Z= 0.319 Chirality : 0.042 0.246 604 Planarity : 0.008 0.143 668 Dihedral : 6.410 53.732 554 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.54 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: 1.85 (0.39), residues: 488 helix: 2.16 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -2.35 (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 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 Details of bonding type rmsd hydrogen bonds : bond 0.04541 ( 316) hydrogen bonds : angle 4.76569 ( 936) SS BOND : bond 0.00119 ( 2) SS BOND : angle 0.62745 ( 4) covalent geometry : bond 0.00352 ( 4060) covalent geometry : angle 0.59429 ( 5526) Misc. bond : bond 0.00167 ( 4) *********************** 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 : 0.456 Fit side-chains REVERT: A 103 LYS cc_start: 0.7178 (mmtm) cc_final: 0.6494 (mtpt) REVERT: A 194 LYS cc_start: 0.7428 (mtpt) cc_final: 0.6576 (mmtt) REVERT: A 273 GLU cc_start: 0.6707 (mt-10) cc_final: 0.6132 (tp30) REVERT: B 103 LYS cc_start: 0.7182 (mmtm) cc_final: 0.6494 (mtpt) REVERT: B 194 LYS cc_start: 0.7101 (mmmt) cc_final: 0.6407 (mtpm) REVERT: B 273 GLU cc_start: 0.6658 (mt-10) cc_final: 0.6095 (tp30) outliers start: 10 outliers final: 2 residues processed: 58 average time/residue: 1.6791 time to fit residues: 100.4933 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 : 0.747 ------------------------------------------------------------------------------- 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: 0.7980 chunk 36 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 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 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 = 0.3456 r_free = 0.3456 target = 0.124456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.109451 restraints weight = 4125.086| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.47 r_work: 0.3166 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4066 Z= 0.160 Angle : 0.592 8.427 5530 Z= 0.316 Chirality : 0.042 0.247 604 Planarity : 0.008 0.142 668 Dihedral : 6.314 53.154 554 Min Nonbonded Distance : 2.443 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: 1.89 (0.39), residues: 488 helix: 2.20 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -2.39 (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 178 TYR 0.014 0.001 TYR A 109 ARG 0.001 0.000 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.04454 ( 316) hydrogen bonds : angle 4.71307 ( 936) SS BOND : bond 0.00094 ( 2) SS BOND : angle 0.61466 ( 4) covalent geometry : bond 0.00341 ( 4060) covalent geometry : angle 0.59177 ( 5526) Misc. bond : bond 0.00160 ( 4) *********************** 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 : 0.412 Fit side-chains REVERT: A 103 LYS cc_start: 0.7168 (mmtm) cc_final: 0.6503 (mtpt) REVERT: A 194 LYS cc_start: 0.7414 (mtpt) cc_final: 0.6556 (mmtt) REVERT: A 273 GLU cc_start: 0.6705 (mt-10) cc_final: 0.6136 (tp30) REVERT: B 103 LYS cc_start: 0.7171 (mmtm) cc_final: 0.6501 (mtpt) REVERT: B 194 LYS cc_start: 0.7082 (mmmt) cc_final: 0.6383 (mtpm) REVERT: B 273 GLU cc_start: 0.6670 (mt-10) cc_final: 0.6108 (tp30) outliers start: 8 outliers final: 0 residues processed: 62 average time/residue: 1.3385 time to fit residues: 85.5730 Evaluate side-chains 55 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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: 0.7980 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 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 = 0.3448 r_free = 0.3448 target = 0.123812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.108704 restraints weight = 4299.886| |-----------------------------------------------------------------------------| r_work (start): 0.3258 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: 3.44 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4066 Z= 0.176 Angle : 0.609 8.609 5530 Z= 0.325 Chirality : 0.043 0.246 604 Planarity : 0.008 0.143 668 Dihedral : 6.129 51.351 552 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.97 % Favored : 92.62 % Rotamer: Outliers : 2.22 % Allowed : 18.72 % Favored : 79.06 % 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 B 201 PHE 0.011 0.002 PHE A 178 TYR 0.014 0.001 TYR B 109 ARG 0.001 0.000 ARG A 268 Details of bonding type rmsd hydrogen bonds : bond 0.04509 ( 316) hydrogen bonds : angle 4.77606 ( 936) SS BOND : bond 0.00595 ( 2) SS BOND : angle 2.49560 ( 4) covalent geometry : bond 0.00383 ( 4060) covalent geometry : angle 0.60536 ( 5526) Misc. bond : bond 0.00176 ( 4) *********************** 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 64 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.448 Fit side-chains REVERT: A 56 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7627 (mt0) REVERT: A 103 LYS cc_start: 0.7227 (mmtm) cc_final: 0.6556 (mtpt) REVERT: A 194 LYS cc_start: 0.7440 (mtpt) cc_final: 0.6582 (mmtt) REVERT: A 273 GLU cc_start: 0.6744 (mt-10) cc_final: 0.6152 (tp30) REVERT: B 56 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7627 (mt0) REVERT: B 103 LYS cc_start: 0.7234 (mmtm) cc_final: 0.6559 (mtpt) REVERT: B 194 LYS cc_start: 0.7094 (mmmt) cc_final: 0.6385 (mtpm) REVERT: B 273 GLU cc_start: 0.6699 (mt-10) cc_final: 0.6128 (tp30) outliers start: 9 outliers final: 4 residues processed: 58 average time/residue: 2.3351 time to fit residues: 138.9871 Evaluate side-chains 61 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 30 optimal weight: 0.2980 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 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 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 = 0.3467 r_free = 0.3467 target = 0.125339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.110385 restraints weight = 4196.644| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.49 r_work: 0.3174 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4066 Z= 0.153 Angle : 0.585 9.348 5530 Z= 0.310 Chirality : 0.042 0.244 604 Planarity : 0.008 0.146 668 Dihedral : 6.138 53.449 552 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.97 % Favored : 92.62 % Rotamer: Outliers : 2.71 % Allowed : 18.23 % Favored : 79.06 % 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: 2.28 (0.26), residues: 378 sheet: None (None), residues: 0 loop : -2.45 (0.56), 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 0.002 PHE A 219 TYR 0.013 0.001 TYR A 109 ARG 0.001 0.000 ARG A 268 Details of bonding type rmsd hydrogen bonds : bond 0.04342 ( 316) hydrogen bonds : angle 4.71171 ( 936) SS BOND : bond 0.00301 ( 2) SS BOND : angle 1.35071 ( 4) covalent geometry : bond 0.00322 ( 4060) covalent geometry : angle 0.58407 ( 5526) Misc. bond : bond 0.00145 ( 4) *********************** 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 71 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.972 Fit side-chains REVERT: A 56 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7549 (mt0) REVERT: A 103 LYS cc_start: 0.7220 (mmtm) cc_final: 0.6582 (mtpt) REVERT: A 194 LYS cc_start: 0.7422 (mtpt) cc_final: 0.6564 (mmtt) REVERT: A 273 GLU cc_start: 0.6725 (mt-10) cc_final: 0.6138 (tp30) REVERT: B 56 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7552 (mt0) REVERT: B 103 LYS cc_start: 0.7230 (mmtm) cc_final: 0.6563 (mtpt) REVERT: B 194 LYS cc_start: 0.7102 (mmmt) cc_final: 0.6394 (mtpm) REVERT: B 273 GLU cc_start: 0.6690 (mt-10) cc_final: 0.6117 (tp30) outliers start: 11 outliers final: 6 residues processed: 65 average time/residue: 1.6181 time to fit residues: 108.5098 Evaluate side-chains 63 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.6980 chunk 40 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 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 A 104 ASN A 137 ASN B 46 ASN B 137 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.124517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.109490 restraints weight = 4200.561| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.49 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: 0.8007 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4066 Z= 0.160 Angle : 0.605 10.816 5530 Z= 0.319 Chirality : 0.042 0.246 604 Planarity : 0.009 0.150 668 Dihedral : 6.109 51.807 552 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.97 % Favored : 92.62 % Rotamer: Outliers : 2.22 % Allowed : 18.47 % 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: 1.95 (0.39), residues: 488 helix: 2.25 (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 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 Details of bonding type rmsd hydrogen bonds : bond 0.04407 ( 316) hydrogen bonds : angle 4.72174 ( 936) SS BOND : bond 0.00242 ( 2) SS BOND : angle 1.21203 ( 4) covalent geometry : bond 0.00339 ( 4060) covalent geometry : angle 0.60469 ( 5526) Misc. bond : bond 0.00156 ( 4) *********************** 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 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 Fit side-chains REVERT: A 56 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7567 (mt0) REVERT: A 103 LYS cc_start: 0.7218 (mmtm) cc_final: 0.6588 (mtpt) REVERT: A 194 LYS cc_start: 0.7411 (mtpt) cc_final: 0.6554 (mmtt) REVERT: A 273 GLU cc_start: 0.6738 (mt-10) cc_final: 0.6141 (tp30) REVERT: B 56 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7570 (mt0) REVERT: B 103 LYS cc_start: 0.7230 (mmtm) cc_final: 0.6559 (mtpt) REVERT: B 194 LYS cc_start: 0.7084 (mmmt) cc_final: 0.6370 (mtpm) REVERT: B 273 GLU cc_start: 0.6710 (mt-10) cc_final: 0.6125 (tp30) outliers start: 9 outliers final: 4 residues processed: 58 average time/residue: 1.3991 time to fit residues: 83.7661 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 : 0.417 ------------------------------------------------------------------------------- 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 139 THR Chi-restraints excluded: chain B residue 34 CYS 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: 0.9980 chunk 32 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 0.0030 chunk 23 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 overall best weight: 0.5990 ------------------------------------------------------------------------------- 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 = 0.3468 r_free = 0.3468 target = 0.125279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.110279 restraints weight = 4190.904| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.49 r_work: 0.3173 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4066 Z= 0.151 Angle : 0.596 11.158 5530 Z= 0.312 Chirality : 0.041 0.247 604 Planarity : 0.009 0.151 668 Dihedral : 6.104 53.133 552 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.79 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: 1.99 (0.39), residues: 488 helix: 2.27 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -2.35 (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 A 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 Details of bonding type rmsd hydrogen bonds : bond 0.04328 ( 316) hydrogen bonds : angle 4.69260 ( 936) SS BOND : bond 0.00203 ( 2) SS BOND : angle 1.02637 ( 4) covalent geometry : bond 0.00316 ( 4060) covalent geometry : angle 0.59598 ( 5526) Misc. bond : bond 0.00141 ( 4) *********************** 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 63 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.432 Fit side-chains REVERT: A 56 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7569 (mt0) REVERT: A 103 LYS cc_start: 0.7270 (mmtm) cc_final: 0.6637 (mtpt) REVERT: A 194 LYS cc_start: 0.7421 (mtpt) cc_final: 0.6564 (mmtt) REVERT: A 273 GLU cc_start: 0.6735 (mt-10) cc_final: 0.6145 (tp30) REVERT: B 56 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7568 (mt0) REVERT: B 103 LYS cc_start: 0.7240 (mmtm) cc_final: 0.6570 (mtpt) REVERT: B 194 LYS cc_start: 0.7092 (mmmt) cc_final: 0.6384 (mtpm) REVERT: B 273 GLU cc_start: 0.6709 (mt-10) cc_final: 0.6130 (tp30) outliers start: 11 outliers final: 8 residues processed: 58 average time/residue: 1.2329 time to fit residues: 73.9829 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 : 0.426 ------------------------------------------------------------------------------- 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: 0.9990 chunk 37 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 44 optimal weight: 0.0770 chunk 17 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 = 0.3468 r_free = 0.3468 target = 0.126082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.111286 restraints weight = 4234.620| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.47 r_work: 0.3182 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4066 Z= 0.144 Angle : 0.594 11.352 5530 Z= 0.310 Chirality : 0.041 0.248 604 Planarity : 0.009 0.151 668 Dihedral : 6.063 53.614 552 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.97 % Favored : 92.62 % Rotamer: Outliers : 2.96 % Allowed : 18.47 % Favored : 78.57 % 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: 2.07 (0.39), residues: 488 helix: 2.32 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -2.31 (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 0.001 PHE A 219 TYR 0.012 0.001 TYR A 109 ARG 0.001 0.000 ARG B 147 Details of bonding type rmsd hydrogen bonds : bond 0.04243 ( 316) hydrogen bonds : angle 4.66219 ( 936) SS BOND : bond 0.00144 ( 2) SS BOND : angle 0.90887 ( 4) covalent geometry : bond 0.00299 ( 4060) covalent geometry : angle 0.59415 ( 5526) Misc. bond : bond 0.00125 ( 4) *********************** 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 68 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.435 Fit side-chains REVERT: A 56 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7529 (mt0) REVERT: A 103 LYS cc_start: 0.7272 (mmtm) cc_final: 0.6633 (mtpt) REVERT: A 194 LYS cc_start: 0.7383 (mtpt) cc_final: 0.6516 (mmtt) REVERT: A 273 GLU cc_start: 0.6701 (mt-10) cc_final: 0.6125 (tp30) REVERT: B 56 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7525 (mt0) REVERT: B 103 LYS cc_start: 0.7214 (mmtm) cc_final: 0.6545 (mtpt) REVERT: B 194 LYS cc_start: 0.7030 (mmmt) cc_final: 0.6433 (mmtt) REVERT: B 273 GLU cc_start: 0.6686 (mt-10) cc_final: 0.6117 (tp30) outliers start: 12 outliers final: 8 residues processed: 62 average time/residue: 1.1675 time to fit residues: 75.0707 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 : 0.444 ------------------------------------------------------------------------------- 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: 0.9980 chunk 30 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 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 = 0.3449 r_free = 0.3449 target = 0.124469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.109582 restraints weight = 4195.073| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.45 r_work: 0.3161 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4066 Z= 0.161 Angle : 0.615 11.658 5530 Z= 0.321 Chirality : 0.042 0.247 604 Planarity : 0.009 0.152 668 Dihedral : 6.078 51.549 552 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.97 % Favored : 92.62 % Rotamer: Outliers : 2.96 % Allowed : 18.47 % Favored : 78.57 % 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: 2.01 (0.39), residues: 488 helix: 2.28 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -2.33 (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 0.011 0.002 PHE A 178 TYR 0.013 0.001 TYR A 109 ARG 0.001 0.000 ARG B 147 Details of bonding type rmsd hydrogen bonds : bond 0.04394 ( 316) hydrogen bonds : angle 4.70460 ( 936) SS BOND : bond 0.00237 ( 2) SS BOND : angle 1.05852 ( 4) covalent geometry : bond 0.00343 ( 4060) covalent geometry : angle 0.61478 ( 5526) Misc. bond : bond 0.00156 ( 4) ********************** 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 : 0.425 Fit side-chains REVERT: A 56 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7518 (mt0) REVERT: A 103 LYS cc_start: 0.7247 (mmtm) cc_final: 0.6580 (mtpt) REVERT: A 194 LYS cc_start: 0.7342 (mtpt) cc_final: 0.6495 (mmtt) REVERT: A 273 GLU cc_start: 0.6714 (mt-10) cc_final: 0.6121 (tp30) REVERT: B 56 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7521 (mt0) REVERT: B 103 LYS cc_start: 0.7192 (mmtm) cc_final: 0.6515 (mtpt) REVERT: B 194 LYS cc_start: 0.7029 (mmmt) cc_final: 0.6317 (mtpm) REVERT: B 273 GLU cc_start: 0.6689 (mt-10) cc_final: 0.6104 (tp30) outliers start: 12 outliers final: 8 residues processed: 58 average time/residue: 1.2978 time to fit residues: 77.8426 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 : 0.421 ------------------------------------------------------------------------------- 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: 0.0770 chunk 19 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.125130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.110321 restraints weight = 4166.131| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.45 r_work: 0.3172 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4066 Z= 0.154 Angle : 0.611 11.695 5530 Z= 0.319 Chirality : 0.042 0.248 604 Planarity : 0.009 0.152 668 Dihedral : 6.092 52.882 552 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 : 2.96 % Allowed : 18.72 % Favored : 78.33 % 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: 2.04 (0.39), residues: 488 helix: 2.29 (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 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 Details of bonding type rmsd hydrogen bonds : bond 0.04336 ( 316) hydrogen bonds : angle 4.68204 ( 936) SS BOND : bond 0.00187 ( 2) SS BOND : angle 0.96351 ( 4) covalent geometry : bond 0.00326 ( 4060) covalent geometry : angle 0.61084 ( 5526) Misc. bond : bond 0.00143 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5283.67 seconds wall clock time: 92 minutes 48.34 seconds (5568.34 seconds total)