Starting phenix.real_space_refine on Wed Jul 23 07:47:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pjp_17718/07_2025/8pjp_17718.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pjp_17718/07_2025/8pjp_17718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pjp_17718/07_2025/8pjp_17718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pjp_17718/07_2025/8pjp_17718.map" model { file = "/net/cci-nas-00/data/ceres_data/8pjp_17718/07_2025/8pjp_17718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pjp_17718/07_2025/8pjp_17718.cif" } resolution = 2.92 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= 0.002 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 9 5.16 5 C 1342 2.51 5 N 371 2.21 5 O 434 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 2157 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1197 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 931 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {'G3P': 1, 'WKE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.16, per 1000 atoms: 1.46 Number of scatterers: 2157 At special positions: 0 Unit cell: (61.06, 71.38, 111.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 P 1 15.00 O 434 8.00 N 371 7.00 C 1342 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 154 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 98 " 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 275.5 milliseconds 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 516 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 5 sheets defined 26.2% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 2 through 18 removed outlier: 3.523A pdb=" N LEU A 6 " --> pdb=" O THR A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 42 removed outlier: 4.376A pdb=" N TYR A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 55 removed outlier: 3.569A pdb=" N VAL A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 146 through 150 Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.517A pdb=" N THR C 93 " --> pdb=" O PRO C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 113 Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 83 removed outlier: 3.797A pdb=" N SER A 79 " --> pdb=" O GLN A 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 125 removed outlier: 3.511A pdb=" N ALA A 135 " --> pdb=" O THR A 125 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 6 through 9 removed outlier: 4.091A pdb=" N THR C 80 " --> pdb=" O ASP C 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.986A pdb=" N ILE C 36 " --> pdb=" O CYS C 52 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N CYS C 52 " --> pdb=" O ILE C 36 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TRP C 38 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 13 through 14 removed outlier: 7.034A pdb=" N ALA C 100 " --> pdb=" O ASP C 116 " (cutoff:3.500A) 95 hydrogen bonds defined for protein. 249 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: 0.57 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 709 1.34 - 1.46: 348 1.46 - 1.57: 1121 1.57 - 1.69: 1 1.69 - 1.81: 13 Bond restraints: 2192 Sorted by residual: bond pdb=" O1P G3P A 201 " pdb=" P G3P A 201 " ideal model delta sigma weight residual 1.726 1.609 0.117 2.00e-02 2.50e+03 3.44e+01 bond pdb=" C6 WKE A 202 " pdb=" O6 WKE A 202 " ideal model delta sigma weight residual 1.401 1.433 -0.032 2.00e-02 2.50e+03 2.48e+00 bond pdb=" C8 WKE A 202 " pdb=" C9 WKE A 202 " ideal model delta sigma weight residual 1.531 1.500 0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" C10 WKE A 202 " pdb=" O5 WKE A 202 " ideal model delta sigma weight residual 1.405 1.432 -0.027 2.00e-02 2.50e+03 1.79e+00 bond pdb=" C9 WKE A 202 " pdb=" O4 WKE A 202 " ideal model delta sigma weight residual 1.404 1.431 -0.027 2.00e-02 2.50e+03 1.79e+00 ... (remaining 2187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 2941 1.82 - 3.64: 25 3.64 - 5.46: 6 5.46 - 7.28: 4 7.28 - 9.10: 1 Bond angle restraints: 2977 Sorted by residual: angle pdb=" O1P G3P A 201 " pdb=" P G3P A 201 " pdb=" O4P G3P A 201 " ideal model delta sigma weight residual 100.65 109.75 -9.10 3.00e+00 1.11e-01 9.20e+00 angle pdb=" O2P G3P A 201 " pdb=" P G3P A 201 " pdb=" O4P G3P A 201 " ideal model delta sigma weight residual 115.71 109.69 6.02 3.00e+00 1.11e-01 4.02e+00 angle pdb=" C SER A 62 " pdb=" N SER A 63 " pdb=" CA SER A 63 " ideal model delta sigma weight residual 122.60 119.64 2.96 1.56e+00 4.11e-01 3.59e+00 angle pdb=" O3P G3P A 201 " pdb=" P G3P A 201 " pdb=" O4P G3P A 201 " ideal model delta sigma weight residual 115.20 109.66 5.54 3.00e+00 1.11e-01 3.42e+00 angle pdb=" O1P G3P A 201 " pdb=" P G3P A 201 " pdb=" O3P G3P A 201 " ideal model delta sigma weight residual 104.20 109.74 -5.54 3.00e+00 1.11e-01 3.41e+00 ... (remaining 2972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 1147 16.87 - 33.73: 119 33.73 - 50.60: 43 50.60 - 67.46: 7 67.46 - 84.33: 3 Dihedral angle restraints: 1319 sinusoidal: 507 harmonic: 812 Sorted by residual: dihedral pdb=" CB CYS C 24 " pdb=" SG CYS C 24 " pdb=" SG CYS C 98 " pdb=" CB CYS C 98 " ideal model delta sinusoidal sigma weight residual 93.00 55.87 37.13 1 1.00e+01 1.00e-02 1.95e+01 dihedral pdb=" CB GLU A 35 " pdb=" CG GLU A 35 " pdb=" CD GLU A 35 " pdb=" OE1 GLU A 35 " ideal model delta sinusoidal sigma weight residual 0.00 -84.33 84.33 1 3.00e+01 1.11e-03 9.61e+00 dihedral pdb=" N LYS A 101 " pdb=" CA LYS A 101 " pdb=" CB LYS A 101 " pdb=" CG LYS A 101 " ideal model delta sinusoidal sigma weight residual -60.00 -113.55 53.55 3 1.50e+01 4.44e-03 9.21e+00 ... (remaining 1316 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 212 0.025 - 0.050: 69 0.050 - 0.074: 35 0.074 - 0.099: 13 0.099 - 0.124: 16 Chirality restraints: 345 Sorted by residual: chirality pdb=" CA ILE C 105 " pdb=" N ILE C 105 " pdb=" C ILE C 105 " pdb=" CB ILE C 105 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 chirality pdb=" CA VAL C 95 " pdb=" N VAL C 95 " pdb=" C VAL C 95 " pdb=" CB VAL C 95 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.46e-01 chirality pdb=" CA VAL A 80 " pdb=" N VAL A 80 " pdb=" C VAL A 80 " pdb=" CB VAL A 80 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.42e-01 ... (remaining 342 not shown) Planarity restraints: 380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7 WKE A 202 " 0.053 2.00e-02 2.50e+03 4.32e-02 2.34e+01 pdb=" C8 WKE A 202 " -0.015 2.00e-02 2.50e+03 pdb=" C9 WKE A 202 " 0.040 2.00e-02 2.50e+03 pdb=" N1 WKE A 202 " -0.068 2.00e-02 2.50e+03 pdb=" O3 WKE A 202 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N WKE A 202 " -0.019 2.00e-02 2.50e+03 1.21e-02 1.83e+00 pdb=" C3 WKE A 202 " 0.014 2.00e-02 2.50e+03 pdb=" C4 WKE A 202 " -0.004 2.00e-02 2.50e+03 pdb=" C5 WKE A 202 " -0.004 2.00e-02 2.50e+03 pdb=" O1 WKE A 202 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 21 " -0.015 5.00e-02 4.00e+02 2.29e-02 8.42e-01 pdb=" N PRO A 22 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO A 22 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 22 " -0.013 5.00e-02 4.00e+02 ... (remaining 377 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 794 2.87 - 3.38: 1665 3.38 - 3.89: 3277 3.89 - 4.39: 3602 4.39 - 4.90: 6594 Nonbonded interactions: 15932 Sorted by model distance: nonbonded pdb=" O ASP C 32 " pdb=" OG SER C 55 " model vdw 2.365 3.040 nonbonded pdb=" NH2 ARG C 69 " pdb=" OD2 ASP C 92 " model vdw 2.456 3.120 nonbonded pdb=" N ASP C 116 " pdb=" OD1 ASP C 116 " model vdw 2.482 3.120 nonbonded pdb=" C3 G3P A 201 " pdb=" O1 G3P A 201 " model vdw 2.541 2.752 nonbonded pdb=" OE2 GLU A 49 " pdb=" ND2 ASN A 53 " model vdw 2.542 3.120 ... (remaining 15927 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 2.390 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.510 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:12.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 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 : 0.004 0.117 2196 Z= 0.227 Angle : 0.528 9.098 2981 Z= 0.244 Chirality : 0.040 0.124 345 Planarity : 0.003 0.043 380 Dihedral : 15.916 84.330 797 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.34 % Allowed : 18.75 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.52), residues: 282 helix: 1.00 (0.70), residues: 59 sheet: 0.81 (0.60), residues: 71 loop : 0.35 (0.55), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 108 HIS 0.001 0.000 HIS A 149 PHE 0.002 0.000 PHE A 1 TYR 0.005 0.000 TYR C 97 ARG 0.001 0.000 ARG A 155 Details of bonding type rmsd hydrogen bonds : bond 0.22387 ( 90) hydrogen bonds : angle 7.11717 ( 249) SS BOND : bond 0.00111 ( 2) SS BOND : angle 0.29764 ( 4) covalent geometry : bond 0.00342 ( 2192) covalent geometry : angle 0.52852 ( 2977) Misc. bond : bond 0.04980 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.264 Fit side-chains REVERT: A 132 THR cc_start: 0.9216 (p) cc_final: 0.9013 (t) outliers start: 3 outliers final: 1 residues processed: 77 average time/residue: 0.8688 time to fit residues: 68.6362 Evaluate side-chains 64 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.076459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.048583 restraints weight = 4696.905| |-----------------------------------------------------------------------------| r_work (start): 0.2496 rms_B_bonded: 2.76 r_work: 0.2379 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2267 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9019 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 2196 Z= 0.253 Angle : 0.641 7.076 2981 Z= 0.326 Chirality : 0.045 0.145 345 Planarity : 0.003 0.020 380 Dihedral : 4.805 31.631 340 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 6.70 % Allowed : 22.77 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.52), residues: 282 helix: 0.99 (0.71), residues: 59 sheet: 0.70 (0.62), residues: 72 loop : 0.19 (0.55), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.002 0.001 HIS A 149 PHE 0.013 0.002 PHE C 29 TYR 0.010 0.001 TYR C 97 ARG 0.003 0.000 ARG C 21 Details of bonding type rmsd hydrogen bonds : bond 0.05122 ( 90) hydrogen bonds : angle 4.73946 ( 249) SS BOND : bond 0.00238 ( 2) SS BOND : angle 0.57448 ( 4) covalent geometry : bond 0.00599 ( 2192) covalent geometry : angle 0.64073 ( 2977) Misc. bond : bond 0.00333 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: A 142 ASP cc_start: 0.9119 (p0) cc_final: 0.8716 (p0) REVERT: C 75 ASP cc_start: 0.8543 (t0) cc_final: 0.8105 (t0) REVERT: C 78 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8137 (ptpp) REVERT: C 79 ASN cc_start: 0.9098 (m110) cc_final: 0.8869 (m110) REVERT: C 92 ASP cc_start: 0.8913 (m-30) cc_final: 0.8529 (m-30) outliers start: 15 outliers final: 7 residues processed: 78 average time/residue: 0.8536 time to fit residues: 68.2652 Evaluate side-chains 72 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 122 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 6 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 1 optimal weight: 0.2980 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.077212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.049541 restraints weight = 4688.676| |-----------------------------------------------------------------------------| r_work (start): 0.2508 rms_B_bonded: 2.78 r_work: 0.2388 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2276 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2196 Z= 0.182 Angle : 0.596 7.895 2981 Z= 0.298 Chirality : 0.043 0.139 345 Planarity : 0.003 0.020 380 Dihedral : 4.583 36.478 339 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.91 % Allowed : 25.45 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.52), residues: 282 helix: 1.10 (0.72), residues: 59 sheet: 0.85 (0.61), residues: 72 loop : -0.00 (0.53), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 108 HIS 0.001 0.001 HIS A 149 PHE 0.004 0.001 PHE C 70 TYR 0.006 0.001 TYR C 97 ARG 0.002 0.000 ARG C 21 Details of bonding type rmsd hydrogen bonds : bond 0.04220 ( 90) hydrogen bonds : angle 4.38581 ( 249) SS BOND : bond 0.00107 ( 2) SS BOND : angle 0.39620 ( 4) covalent geometry : bond 0.00433 ( 2192) covalent geometry : angle 0.59663 ( 2977) Misc. bond : bond 0.00340 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 142 ASP cc_start: 0.9127 (p0) cc_final: 0.8744 (p0) REVERT: C 46 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8331 (tp30) REVERT: C 75 ASP cc_start: 0.8573 (t0) cc_final: 0.8088 (t0) REVERT: C 78 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8233 (ptpp) REVERT: C 88 LEU cc_start: 0.9292 (mm) cc_final: 0.9003 (mm) outliers start: 11 outliers final: 9 residues processed: 71 average time/residue: 0.9042 time to fit residues: 65.8513 Evaluate side-chains 72 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 116 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 0.0870 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.077855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.050073 restraints weight = 4665.850| |-----------------------------------------------------------------------------| r_work (start): 0.2529 rms_B_bonded: 2.79 r_work: 0.2413 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2302 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2196 Z= 0.130 Angle : 0.575 8.705 2981 Z= 0.285 Chirality : 0.042 0.133 345 Planarity : 0.003 0.020 380 Dihedral : 4.450 37.370 339 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.02 % Allowed : 26.34 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.52), residues: 282 helix: 1.16 (0.72), residues: 59 sheet: 1.04 (0.62), residues: 72 loop : -0.00 (0.54), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 108 HIS 0.001 0.001 HIS A 149 PHE 0.013 0.001 PHE C 29 TYR 0.006 0.001 TYR C 97 ARG 0.004 0.000 ARG C 21 Details of bonding type rmsd hydrogen bonds : bond 0.03532 ( 90) hydrogen bonds : angle 4.19800 ( 249) SS BOND : bond 0.00103 ( 2) SS BOND : angle 0.36745 ( 4) covalent geometry : bond 0.00308 ( 2192) covalent geometry : angle 0.57540 ( 2977) Misc. bond : bond 0.00307 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 142 ASP cc_start: 0.9116 (p0) cc_final: 0.8751 (p0) REVERT: C 46 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8268 (tp30) REVERT: C 75 ASP cc_start: 0.8626 (t0) cc_final: 0.8151 (t0) REVERT: C 78 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8209 (ptpp) REVERT: C 88 LEU cc_start: 0.9284 (mm) cc_final: 0.9008 (mm) outliers start: 9 outliers final: 7 residues processed: 69 average time/residue: 0.9129 time to fit residues: 64.5556 Evaluate side-chains 68 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 116 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 4 optimal weight: 0.1980 chunk 5 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.077636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.049945 restraints weight = 4777.491| |-----------------------------------------------------------------------------| r_work (start): 0.2523 rms_B_bonded: 2.85 r_work: 0.2405 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2291 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2196 Z= 0.138 Angle : 0.581 8.997 2981 Z= 0.288 Chirality : 0.042 0.134 345 Planarity : 0.003 0.021 380 Dihedral : 4.469 39.776 339 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.91 % Allowed : 24.11 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.52), residues: 282 helix: 1.14 (0.72), residues: 59 sheet: 1.11 (0.63), residues: 71 loop : -0.05 (0.53), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 108 HIS 0.001 0.001 HIS A 149 PHE 0.012 0.001 PHE C 29 TYR 0.006 0.001 TYR C 97 ARG 0.004 0.000 ARG C 21 Details of bonding type rmsd hydrogen bonds : bond 0.03565 ( 90) hydrogen bonds : angle 4.16375 ( 249) SS BOND : bond 0.00116 ( 2) SS BOND : angle 0.40439 ( 4) covalent geometry : bond 0.00328 ( 2192) covalent geometry : angle 0.58115 ( 2977) Misc. bond : bond 0.00304 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 142 ASP cc_start: 0.9144 (p0) cc_final: 0.8815 (p0) REVERT: C 46 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8289 (tp30) REVERT: C 75 ASP cc_start: 0.8575 (t0) cc_final: 0.8080 (t0) REVERT: C 78 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8212 (ptpp) REVERT: C 88 LEU cc_start: 0.9191 (mm) cc_final: 0.8869 (mm) outliers start: 11 outliers final: 10 residues processed: 68 average time/residue: 0.9904 time to fit residues: 69.0046 Evaluate side-chains 71 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 116 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 6 optimal weight: 0.0000 chunk 26 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 20 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.079278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.051732 restraints weight = 4744.590| |-----------------------------------------------------------------------------| r_work (start): 0.2567 rms_B_bonded: 2.85 r_work: 0.2449 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2336 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 2196 Z= 0.100 Angle : 0.563 9.349 2981 Z= 0.278 Chirality : 0.041 0.128 345 Planarity : 0.003 0.021 380 Dihedral : 4.262 37.904 339 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.57 % Allowed : 27.23 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.52), residues: 282 helix: 1.21 (0.72), residues: 59 sheet: 1.30 (0.60), residues: 77 loop : -0.18 (0.55), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 108 HIS 0.001 0.000 HIS A 149 PHE 0.002 0.001 PHE C 70 TYR 0.005 0.001 TYR C 97 ARG 0.004 0.000 ARG C 21 Details of bonding type rmsd hydrogen bonds : bond 0.02787 ( 90) hydrogen bonds : angle 4.00837 ( 249) SS BOND : bond 0.00136 ( 2) SS BOND : angle 0.38567 ( 4) covalent geometry : bond 0.00234 ( 2192) covalent geometry : angle 0.56363 ( 2977) Misc. bond : bond 0.00251 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 142 ASP cc_start: 0.9167 (p0) cc_final: 0.8866 (p0) REVERT: C 46 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8272 (tp30) REVERT: C 75 ASP cc_start: 0.8566 (t0) cc_final: 0.8078 (t0) REVERT: C 78 LYS cc_start: 0.8548 (mtmm) cc_final: 0.8224 (ptpp) REVERT: C 88 LEU cc_start: 0.9186 (mm) cc_final: 0.8860 (mm) outliers start: 8 outliers final: 5 residues processed: 70 average time/residue: 0.9116 time to fit residues: 65.4245 Evaluate side-chains 67 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain C residue 87 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.076800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.048940 restraints weight = 4772.195| |-----------------------------------------------------------------------------| r_work (start): 0.2503 rms_B_bonded: 2.85 r_work: 0.2387 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2277 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2196 Z= 0.185 Angle : 0.644 9.798 2981 Z= 0.320 Chirality : 0.044 0.137 345 Planarity : 0.003 0.022 380 Dihedral : 4.736 45.787 339 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.57 % Allowed : 28.57 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.52), residues: 282 helix: 1.00 (0.71), residues: 59 sheet: 1.15 (0.56), residues: 87 loop : -0.22 (0.57), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 108 HIS 0.002 0.000 HIS A 149 PHE 0.010 0.001 PHE C 29 TYR 0.008 0.001 TYR C 97 ARG 0.005 0.000 ARG C 21 Details of bonding type rmsd hydrogen bonds : bond 0.03995 ( 90) hydrogen bonds : angle 4.14191 ( 249) SS BOND : bond 0.00155 ( 2) SS BOND : angle 0.50200 ( 4) covalent geometry : bond 0.00446 ( 2192) covalent geometry : angle 0.64369 ( 2977) Misc. bond : bond 0.00321 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 142 ASP cc_start: 0.9157 (p0) cc_final: 0.8854 (p0) REVERT: C 46 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8271 (tp30) REVERT: C 75 ASP cc_start: 0.8612 (t0) cc_final: 0.8110 (t0) REVERT: C 78 LYS cc_start: 0.8528 (mtmm) cc_final: 0.8170 (ptpp) REVERT: C 88 LEU cc_start: 0.9190 (mm) cc_final: 0.8915 (mm) outliers start: 8 outliers final: 7 residues processed: 68 average time/residue: 1.0173 time to fit residues: 70.7579 Evaluate side-chains 68 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 116 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 0.0470 chunk 12 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 7 optimal weight: 0.0020 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 4 optimal weight: 0.0870 overall best weight: 0.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.079999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.052121 restraints weight = 4845.518| |-----------------------------------------------------------------------------| r_work (start): 0.2583 rms_B_bonded: 2.89 r_work: 0.2467 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2356 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 2196 Z= 0.107 Angle : 0.605 10.223 2981 Z= 0.302 Chirality : 0.041 0.126 345 Planarity : 0.003 0.024 380 Dihedral : 4.357 40.940 339 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.23 % Allowed : 31.25 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.53), residues: 282 helix: 1.10 (0.72), residues: 59 sheet: 1.18 (0.56), residues: 87 loop : -0.03 (0.59), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.011 0.001 PHE C 29 TYR 0.008 0.001 TYR C 117 ARG 0.004 0.000 ARG C 21 Details of bonding type rmsd hydrogen bonds : bond 0.02440 ( 90) hydrogen bonds : angle 3.95774 ( 249) SS BOND : bond 0.00179 ( 2) SS BOND : angle 0.55862 ( 4) covalent geometry : bond 0.00254 ( 2192) covalent geometry : angle 0.60540 ( 2977) Misc. bond : bond 0.00231 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.9275 (tm-30) cc_final: 0.8984 (tm-30) REVERT: A 142 ASP cc_start: 0.9166 (p0) cc_final: 0.8779 (p0) REVERT: C 46 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8227 (tp30) REVERT: C 75 ASP cc_start: 0.8547 (t0) cc_final: 0.8025 (t0) REVERT: C 78 LYS cc_start: 0.8539 (mtmm) cc_final: 0.8193 (ptpp) REVERT: C 88 LEU cc_start: 0.9221 (mm) cc_final: 0.8892 (mm) outliers start: 5 outliers final: 6 residues processed: 70 average time/residue: 0.9368 time to fit residues: 67.2686 Evaluate side-chains 65 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 116 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.077680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.050154 restraints weight = 4757.186| |-----------------------------------------------------------------------------| r_work (start): 0.2530 rms_B_bonded: 2.75 r_work: 0.2413 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2302 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 2196 Z= 0.173 Angle : 0.654 10.474 2981 Z= 0.326 Chirality : 0.043 0.136 345 Planarity : 0.003 0.022 380 Dihedral : 4.601 46.346 339 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.79 % Allowed : 32.14 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.53), residues: 282 helix: 1.00 (0.72), residues: 59 sheet: 1.09 (0.55), residues: 87 loop : -0.06 (0.58), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 108 HIS 0.002 0.000 HIS A 149 PHE 0.003 0.001 PHE C 39 TYR 0.011 0.001 TYR C 117 ARG 0.005 0.000 ARG C 21 Details of bonding type rmsd hydrogen bonds : bond 0.03795 ( 90) hydrogen bonds : angle 4.08195 ( 249) SS BOND : bond 0.00128 ( 2) SS BOND : angle 0.47695 ( 4) covalent geometry : bond 0.00419 ( 2192) covalent geometry : angle 0.65446 ( 2977) Misc. bond : bond 0.00303 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ASP cc_start: 0.9143 (p0) cc_final: 0.8802 (p0) REVERT: C 46 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8290 (tp30) REVERT: C 75 ASP cc_start: 0.8621 (t0) cc_final: 0.8112 (t0) REVERT: C 78 LYS cc_start: 0.8528 (mtmm) cc_final: 0.8163 (ptpp) REVERT: C 88 LEU cc_start: 0.9251 (mm) cc_final: 0.8963 (mm) outliers start: 4 outliers final: 4 residues processed: 65 average time/residue: 1.0250 time to fit residues: 68.2721 Evaluate side-chains 65 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain C residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 0.1980 chunk 26 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.079156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.051540 restraints weight = 4668.083| |-----------------------------------------------------------------------------| r_work (start): 0.2566 rms_B_bonded: 2.82 r_work: 0.2453 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2343 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 2196 Z= 0.117 Angle : 0.622 10.356 2981 Z= 0.310 Chirality : 0.042 0.129 345 Planarity : 0.003 0.022 380 Dihedral : 4.402 44.001 339 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.23 % Allowed : 31.70 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.53), residues: 282 helix: 1.09 (0.73), residues: 59 sheet: 1.18 (0.56), residues: 87 loop : 0.03 (0.59), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 108 HIS 0.001 0.000 HIS A 149 PHE 0.010 0.001 PHE C 29 TYR 0.006 0.001 TYR C 117 ARG 0.005 0.000 ARG C 21 Details of bonding type rmsd hydrogen bonds : bond 0.02732 ( 90) hydrogen bonds : angle 3.92528 ( 249) SS BOND : bond 0.00111 ( 2) SS BOND : angle 0.41508 ( 4) covalent geometry : bond 0.00284 ( 2192) covalent geometry : angle 0.62181 ( 2977) Misc. bond : bond 0.00242 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.9302 (tm-30) cc_final: 0.8972 (tm-30) REVERT: A 142 ASP cc_start: 0.9153 (p0) cc_final: 0.8814 (p0) REVERT: C 46 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8254 (tp30) REVERT: C 75 ASP cc_start: 0.8560 (t0) cc_final: 0.8030 (t0) REVERT: C 78 LYS cc_start: 0.8495 (mtmm) cc_final: 0.8135 (ptpp) REVERT: C 88 LEU cc_start: 0.9220 (mm) cc_final: 0.8872 (mm) outliers start: 5 outliers final: 5 residues processed: 64 average time/residue: 0.9804 time to fit residues: 64.2429 Evaluate side-chains 65 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain C residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 14 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.077217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.049212 restraints weight = 4747.220| |-----------------------------------------------------------------------------| r_work (start): 0.2511 rms_B_bonded: 2.83 r_work: 0.2397 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2288 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2196 Z= 0.183 Angle : 0.691 10.238 2981 Z= 0.349 Chirality : 0.044 0.137 345 Planarity : 0.003 0.031 380 Dihedral : 4.820 48.662 339 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.68 % Allowed : 31.25 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.52), residues: 282 helix: 0.96 (0.72), residues: 59 sheet: 1.10 (0.57), residues: 87 loop : -0.21 (0.56), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 108 HIS 0.002 0.000 HIS A 149 PHE 0.008 0.001 PHE C 29 TYR 0.007 0.001 TYR C 82 ARG 0.005 0.000 ARG C 21 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 90) hydrogen bonds : angle 4.09892 ( 249) SS BOND : bond 0.00113 ( 2) SS BOND : angle 0.46024 ( 4) covalent geometry : bond 0.00443 ( 2192) covalent geometry : angle 0.69107 ( 2977) Misc. bond : bond 0.00311 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2613.57 seconds wall clock time: 45 minutes 22.73 seconds (2722.73 seconds total)