Starting phenix.real_space_refine on Fri May 9 13:38:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pjp_17718/05_2025/8pjp_17718.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pjp_17718/05_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_17718/05_2025/8pjp_17718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pjp_17718/05_2025/8pjp_17718.map" model { file = "/net/cci-nas-00/data/ceres_data/8pjp_17718/05_2025/8pjp_17718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pjp_17718/05_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-5687/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: 3.05, per 1000 atoms: 1.41 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: 0.70 Conformation dependent library (CDL) restraints added in 258.1 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: 0.28 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: 0.54 Time building geometry restraints manager: 0.68 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: 2.630 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.480 Find NCS groups from input model: 0.020 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:12.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.430 ------------------------------------------------------------------------------- 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 : 0.277 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: 0.9117 time to fit residues: 72.0403 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 : 0.229 ------------------------------------------------------------------------------- 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 = 41)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.048578 restraints weight = 4696.946| |-----------------------------------------------------------------------------| r_work (start): 0.2498 rms_B_bonded: 2.77 r_work: 0.2379 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2266 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 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 4.73947 ( 249) SS BOND : bond 0.00238 ( 2) SS BOND : angle 0.57447 ( 4) covalent geometry : bond 0.00599 ( 2192) covalent geometry : angle 0.64072 ( 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 : 0.267 Fit side-chains revert: symmetry clash REVERT: A 142 ASP cc_start: 0.9123 (p0) cc_final: 0.8725 (p0) REVERT: C 75 ASP cc_start: 0.8514 (t0) cc_final: 0.8079 (t0) REVERT: C 78 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8118 (ptpp) REVERT: C 79 ASN cc_start: 0.9098 (m110) cc_final: 0.8865 (m110) REVERT: C 92 ASP cc_start: 0.8894 (m-30) cc_final: 0.8507 (m-30) outliers start: 15 outliers final: 7 residues processed: 78 average time/residue: 0.8959 time to fit residues: 71.6535 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 : 0.223 ------------------------------------------------------------------------------- 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: 6.9990 chunk 18 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 = 0.3083 r_free = 0.3083 target = 0.076220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.048443 restraints weight = 4701.744| |-----------------------------------------------------------------------------| r_work (start): 0.2491 rms_B_bonded: 2.77 r_work: 0.2373 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2261 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9032 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2196 Z= 0.226 Angle : 0.616 7.705 2981 Z= 0.310 Chirality : 0.044 0.143 345 Planarity : 0.003 0.021 380 Dihedral : 4.851 39.691 339 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 5.36 % Allowed : 24.11 % 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: 0.57 (0.51), residues: 282 helix: 1.06 (0.71), residues: 59 sheet: 0.82 (0.61), residues: 72 loop : -0.04 (0.53), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 108 HIS 0.002 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 0.04661 ( 90) hydrogen bonds : angle 4.44295 ( 249) SS BOND : bond 0.00152 ( 2) SS BOND : angle 0.42277 ( 4) covalent geometry : bond 0.00539 ( 2192) covalent geometry : angle 0.61587 ( 2977) Misc. bond : bond 0.00360 ( 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: 12 poor density : 63 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 142 ASP cc_start: 0.9120 (p0) cc_final: 0.8735 (p0) REVERT: C 46 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8338 (tp30) REVERT: C 75 ASP cc_start: 0.8605 (t0) cc_final: 0.8110 (t0) REVERT: C 78 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8250 (ptpp) REVERT: C 88 LEU cc_start: 0.9308 (mm) cc_final: 0.9060 (mm) outliers start: 12 outliers final: 10 residues processed: 71 average time/residue: 0.9062 time to fit residues: 65.9201 Evaluate side-chains 72 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 122 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 7 optimal weight: 0.2980 overall best weight: 2.6588 ------------------------------------------------------------------------------- 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 = 0.3092 r_free = 0.3092 target = 0.076761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.048737 restraints weight = 4664.319| |-----------------------------------------------------------------------------| r_work (start): 0.2498 rms_B_bonded: 2.78 r_work: 0.2379 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2267 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2196 Z= 0.186 Angle : 0.608 8.508 2981 Z= 0.304 Chirality : 0.043 0.138 345 Planarity : 0.003 0.021 380 Dihedral : 4.836 43.091 339 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % 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: 0.60 (0.52), residues: 282 helix: 1.02 (0.71), residues: 59 sheet: 0.97 (0.62), residues: 72 loop : -0.06 (0.53), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 108 HIS 0.002 0.001 HIS A 149 PHE 0.013 0.001 PHE C 29 TYR 0.007 0.001 TYR C 97 ARG 0.004 0.000 ARG C 21 Details of bonding type rmsd hydrogen bonds : bond 0.04195 ( 90) hydrogen bonds : angle 4.30837 ( 249) SS BOND : bond 0.00137 ( 2) SS BOND : angle 0.41654 ( 4) covalent geometry : bond 0.00445 ( 2192) covalent geometry : angle 0.60827 ( 2977) Misc. bond : bond 0.00348 ( 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 75 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 142 ASP cc_start: 0.9136 (p0) cc_final: 0.8801 (p0) REVERT: C 15 GLN cc_start: 0.8928 (pm20) cc_final: 0.8481 (pm20) REVERT: C 46 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8286 (tp30) REVERT: C 75 ASP cc_start: 0.8569 (t0) cc_final: 0.8053 (t0) REVERT: C 78 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8141 (ptpp) REVERT: C 88 LEU cc_start: 0.9307 (mm) cc_final: 0.9025 (mm) outliers start: 11 outliers final: 9 residues processed: 72 average time/residue: 0.8993 time to fit residues: 66.3258 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 : 0.248 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 8 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 = 0.3090 r_free = 0.3090 target = 0.076318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.048301 restraints weight = 4801.642| |-----------------------------------------------------------------------------| r_work (start): 0.2489 rms_B_bonded: 2.87 r_work: 0.2370 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2258 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2196 Z= 0.191 Angle : 0.611 9.291 2981 Z= 0.304 Chirality : 0.044 0.138 345 Planarity : 0.003 0.020 380 Dihedral : 4.947 47.665 339 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 5.36 % Allowed : 24.11 % 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: 0.54 (0.52), residues: 282 helix: 0.94 (0.70), residues: 59 sheet: 1.01 (0.64), residues: 71 loop : -0.13 (0.53), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 108 HIS 0.001 0.000 HIS A 149 PHE 0.012 0.001 PHE C 29 TYR 0.007 0.001 TYR C 97 ARG 0.003 0.000 ARG C 21 Details of bonding type rmsd hydrogen bonds : bond 0.04221 ( 90) hydrogen bonds : angle 4.26570 ( 249) SS BOND : bond 0.00152 ( 2) SS BOND : angle 0.44315 ( 4) covalent geometry : bond 0.00458 ( 2192) covalent geometry : angle 0.61096 ( 2977) Misc. bond : bond 0.00345 ( 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 74 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 142 ASP cc_start: 0.9164 (p0) cc_final: 0.8877 (p0) REVERT: C 15 GLN cc_start: 0.8966 (pm20) cc_final: 0.8500 (pm20) REVERT: C 40 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.8134 (ttm170) REVERT: C 46 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8290 (tp30) REVERT: C 75 ASP cc_start: 0.8575 (t0) cc_final: 0.8091 (t0) REVERT: C 78 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8173 (ptpp) REVERT: C 88 LEU cc_start: 0.9281 (mm) cc_final: 0.8983 (mm) outliers start: 12 outliers final: 9 residues processed: 71 average time/residue: 0.9687 time to fit residues: 70.3879 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 : 0.213 ------------------------------------------------------------------------------- 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 105 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 0.0470 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 23 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- 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 = 0.3139 r_free = 0.3139 target = 0.078895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.051125 restraints weight = 4742.600| |-----------------------------------------------------------------------------| r_work (start): 0.2555 rms_B_bonded: 2.87 r_work: 0.2437 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2325 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 2196 Z= 0.106 Angle : 0.565 9.576 2981 Z= 0.279 Chirality : 0.041 0.130 345 Planarity : 0.003 0.021 380 Dihedral : 4.521 45.246 339 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.75 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: 0.71 (0.53), residues: 282 helix: 1.14 (0.72), residues: 59 sheet: 1.10 (0.56), residues: 87 loop : -0.19 (0.58), 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 0.012 0.001 PHE C 29 TYR 0.004 0.001 TYR A 50 ARG 0.004 0.000 ARG C 21 Details of bonding type rmsd hydrogen bonds : bond 0.02783 ( 90) hydrogen bonds : angle 4.01372 ( 249) SS BOND : bond 0.00139 ( 2) SS BOND : angle 0.42730 ( 4) covalent geometry : bond 0.00248 ( 2192) covalent geometry : angle 0.56486 ( 2977) Misc. bond : bond 0.00268 ( 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 72 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 142 ASP cc_start: 0.9158 (p0) cc_final: 0.8890 (p0) REVERT: C 15 GLN cc_start: 0.8879 (pm20) cc_final: 0.8381 (pm20) REVERT: C 46 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8262 (tp30) REVERT: C 75 ASP cc_start: 0.8732 (t0) cc_final: 0.8124 (t0) REVERT: C 78 LYS cc_start: 0.8528 (mtmm) cc_final: 0.8101 (ptpp) REVERT: C 88 LEU cc_start: 0.9231 (mm) cc_final: 0.8907 (mm) outliers start: 8 outliers final: 4 residues processed: 70 average time/residue: 0.9324 time to fit residues: 67.0768 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 : 0.223 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 21 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3128 r_free = 0.3128 target = 0.078270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.050725 restraints weight = 4784.182| |-----------------------------------------------------------------------------| r_work (start): 0.2540 rms_B_bonded: 2.84 r_work: 0.2421 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2308 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2196 Z= 0.121 Angle : 0.597 10.018 2981 Z= 0.294 Chirality : 0.042 0.131 345 Planarity : 0.003 0.022 380 Dihedral : 4.539 46.870 339 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.57 % Allowed : 28.12 % Favored : 68.30 % 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: 1.12 (0.72), residues: 59 sheet: 1.12 (0.56), residues: 87 loop : -0.15 (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 0.011 0.001 PHE C 29 TYR 0.005 0.001 TYR C 97 ARG 0.005 0.000 ARG C 21 Details of bonding type rmsd hydrogen bonds : bond 0.03133 ( 90) hydrogen bonds : angle 4.03688 ( 249) SS BOND : bond 0.00117 ( 2) SS BOND : angle 0.44142 ( 4) covalent geometry : bond 0.00291 ( 2192) covalent geometry : angle 0.59733 ( 2977) Misc. bond : bond 0.00272 ( 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 : 0.226 Fit side-chains revert: symmetry clash REVERT: A 142 ASP cc_start: 0.9161 (p0) cc_final: 0.8816 (p0) REVERT: C 15 GLN cc_start: 0.8885 (pm20) cc_final: 0.8395 (pm20) REVERT: C 46 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8267 (tp30) REVERT: C 75 ASP cc_start: 0.8666 (t0) cc_final: 0.8151 (t0) REVERT: C 78 LYS cc_start: 0.8522 (mtmm) cc_final: 0.8154 (ptpp) REVERT: C 88 LEU cc_start: 0.9254 (mm) cc_final: 0.8951 (mm) outliers start: 8 outliers final: 5 residues processed: 68 average time/residue: 0.9822 time to fit residues: 68.3355 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 : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 5.9990 chunk 25 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.079161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.051325 restraints weight = 4830.425| |-----------------------------------------------------------------------------| r_work (start): 0.2557 rms_B_bonded: 2.86 r_work: 0.2438 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2325 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 2196 Z= 0.113 Angle : 0.609 10.295 2981 Z= 0.302 Chirality : 0.042 0.129 345 Planarity : 0.003 0.023 380 Dihedral : 4.453 46.041 339 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.68 % Allowed : 29.91 % Favored : 67.41 % 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: 1.02 (0.53), residues: 282 helix: 1.78 (0.75), residues: 53 sheet: 1.14 (0.56), residues: 87 loop : 0.02 (0.57), residues: 142 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 0.011 0.001 PHE C 29 TYR 0.004 0.001 TYR A 50 ARG 0.004 0.000 ARG C 21 Details of bonding type rmsd hydrogen bonds : bond 0.02770 ( 90) hydrogen bonds : angle 3.93874 ( 249) SS BOND : bond 0.00089 ( 2) SS BOND : angle 0.53039 ( 4) covalent geometry : bond 0.00271 ( 2192) covalent geometry : angle 0.60894 ( 2977) Misc. bond : bond 0.00245 ( 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 67 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.9303 (tm-30) cc_final: 0.8956 (tm-30) REVERT: A 142 ASP cc_start: 0.9169 (p0) cc_final: 0.8839 (p0) REVERT: C 15 GLN cc_start: 0.8894 (pm20) cc_final: 0.8402 (pm20) REVERT: C 46 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8283 (tp30) REVERT: C 75 ASP cc_start: 0.8617 (t0) cc_final: 0.7991 (t0) REVERT: C 78 LYS cc_start: 0.8512 (mtmm) cc_final: 0.8085 (ptpp) REVERT: C 88 LEU cc_start: 0.9271 (mm) cc_final: 0.8939 (mm) outliers start: 6 outliers final: 6 residues processed: 67 average time/residue: 0.9615 time to fit residues: 65.9655 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 : 0.224 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 30.0000 chunk 25 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.077468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.049385 restraints weight = 4734.785| |-----------------------------------------------------------------------------| r_work (start): 0.2513 rms_B_bonded: 2.83 r_work: 0.2397 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2286 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.3338 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= 0.165 Angle : 0.649 10.217 2981 Z= 0.323 Chirality : 0.043 0.135 345 Planarity : 0.003 0.020 380 Dihedral : 4.778 50.309 339 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.68 % Allowed : 30.36 % Favored : 66.96 % 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: 0.69 (0.53), residues: 282 helix: 1.00 (0.73), residues: 59 sheet: 1.05 (0.56), residues: 87 loop : -0.11 (0.58), 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 0.003 0.001 PHE C 39 TYR 0.006 0.001 TYR C 97 ARG 0.005 0.000 ARG C 21 Details of bonding type rmsd hydrogen bonds : bond 0.03713 ( 90) hydrogen bonds : angle 4.09452 ( 249) SS BOND : bond 0.00096 ( 2) SS BOND : angle 0.43160 ( 4) covalent geometry : bond 0.00399 ( 2192) covalent geometry : angle 0.64935 ( 2977) Misc. bond : bond 0.00306 ( 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 68 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ASP cc_start: 0.9176 (p0) cc_final: 0.8851 (p0) REVERT: C 46 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8290 (tp30) REVERT: C 75 ASP cc_start: 0.8603 (t0) cc_final: 0.7983 (t0) REVERT: C 78 LYS cc_start: 0.8487 (mtmm) cc_final: 0.8054 (ptpp) REVERT: C 88 LEU cc_start: 0.9281 (mm) cc_final: 0.8997 (mm) outliers start: 6 outliers final: 6 residues processed: 68 average time/residue: 0.9356 time to fit residues: 65.1945 Evaluate side-chains 68 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3125 r_free = 0.3125 target = 0.078356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.050522 restraints weight = 4653.147| |-----------------------------------------------------------------------------| r_work (start): 0.2543 rms_B_bonded: 2.81 r_work: 0.2427 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2315 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 2196 Z= 0.128 Angle : 0.623 10.181 2981 Z= 0.311 Chirality : 0.042 0.133 345 Planarity : 0.003 0.022 380 Dihedral : 4.627 49.214 339 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.57 % Allowed : 29.91 % 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: 0.80 (0.53), residues: 282 helix: 1.07 (0.73), residues: 59 sheet: 1.11 (0.56), residues: 87 loop : -0.02 (0.58), 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 0.009 0.001 PHE C 29 TYR 0.004 0.001 TYR C 97 ARG 0.005 0.000 ARG C 21 Details of bonding type rmsd hydrogen bonds : bond 0.03029 ( 90) hydrogen bonds : angle 3.97264 ( 249) SS BOND : bond 0.00107 ( 2) SS BOND : angle 0.40740 ( 4) covalent geometry : bond 0.00309 ( 2192) covalent geometry : angle 0.62287 ( 2977) Misc. bond : bond 0.00267 ( 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 68 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.9310 (tm-30) cc_final: 0.8923 (tm-30) REVERT: A 142 ASP cc_start: 0.9176 (p0) cc_final: 0.8849 (p0) REVERT: C 46 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8275 (tp30) REVERT: C 75 ASP cc_start: 0.8576 (t0) cc_final: 0.7965 (t0) REVERT: C 78 LYS cc_start: 0.8463 (mtmm) cc_final: 0.8036 (ptpp) REVERT: C 88 LEU cc_start: 0.9269 (mm) cc_final: 0.8886 (mm) outliers start: 8 outliers final: 7 residues processed: 67 average time/residue: 0.9574 time to fit residues: 65.6723 Evaluate side-chains 67 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 55 SER 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: 3.9990 chunk 10 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 13 optimal weight: 0.0470 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 overall best weight: 1.6084 ------------------------------------------------------------------------------- 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 = 0.3117 r_free = 0.3117 target = 0.077981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.050025 restraints weight = 4755.311| |-----------------------------------------------------------------------------| r_work (start): 0.2530 rms_B_bonded: 2.83 r_work: 0.2415 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2305 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.3395 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= 0.140 Angle : 0.639 10.201 2981 Z= 0.318 Chirality : 0.043 0.133 345 Planarity : 0.003 0.021 380 Dihedral : 4.685 50.102 339 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.12 % Allowed : 30.36 % 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: 0.77 (0.53), residues: 282 helix: 1.03 (0.73), residues: 59 sheet: 1.08 (0.57), 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 0.003 0.001 PHE A 119 TYR 0.006 0.001 TYR C 97 ARG 0.005 0.000 ARG C 21 Details of bonding type rmsd hydrogen bonds : bond 0.03273 ( 90) hydrogen bonds : angle 4.01713 ( 249) SS BOND : bond 0.00101 ( 2) SS BOND : angle 0.41974 ( 4) covalent geometry : bond 0.00342 ( 2192) covalent geometry : angle 0.63928 ( 2977) Misc. bond : bond 0.00280 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2592.44 seconds wall clock time: 45 minutes 27.35 seconds (2727.35 seconds total)