Starting phenix.real_space_refine on Fri May 9 14:46:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jex_36202/05_2025/8jex_36202.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jex_36202/05_2025/8jex_36202.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jex_36202/05_2025/8jex_36202.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jex_36202/05_2025/8jex_36202.map" model { file = "/net/cci-nas-00/data/ceres_data/8jex_36202/05_2025/8jex_36202.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jex_36202/05_2025/8jex_36202.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 3 Type Number sf(0) Gaussians C 1614 2.51 5 N 450 2.21 5 O 552 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: 2616 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 377 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: D, I, J, L, Q, B, G, H, K, P Time building chain proxies: 2.05, per 1000 atoms: 0.78 Number of scatterers: 2616 At special positions: 0 Unit cell: (112.05, 126.99, 31.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 552 8.00 N 450 7.00 C 1614 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=0, symmetry=0 Links applied NAG-SER " NAG A 201 " - " SER A 87 " " NAG B 201 " - " SER B 87 " " NAG G 201 " - " SER G 87 " " NAG H 201 " - " SER H 87 " " NAG K 201 " - " SER K 87 " " NAG P 201 " - " SER P 87 " Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 359.3 milliseconds 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 660 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'H' and resid 40 through 44 Processing sheet with id=AA2, first strand: chain 'H' and resid 50 through 51 removed outlier: 6.458A pdb=" N HIS H 50 " --> pdb=" O GLY P 51 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N HIS P 50 " --> pdb=" O GLY G 51 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'H' and resid 63 through 66 Processing sheet with id=AA4, first strand: chain 'H' and resid 70 through 72 Processing sheet with id=AA5, first strand: chain 'H' and resid 76 through 79 removed outlier: 6.453A pdb=" N ALA H 76 " --> pdb=" O VAL P 77 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N GLN P 79 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA H 78 " --> pdb=" O GLN P 79 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA P 76 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N GLN G 79 " --> pdb=" O ALA P 76 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA P 78 " --> pdb=" O GLN G 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 40 through 44 Processing sheet with id=AA7, first strand: chain 'B' and resid 50 through 51 removed outlier: 6.458A pdb=" N HIS B 50 " --> pdb=" O GLY K 51 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N HIS K 50 " --> pdb=" O GLY A 51 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 63 through 66 Processing sheet with id=AA9, first strand: chain 'B' and resid 70 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 76 through 79 removed outlier: 6.452A pdb=" N ALA B 76 " --> pdb=" O VAL K 77 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N GLN K 79 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA B 78 " --> pdb=" O GLN K 79 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA K 76 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N GLN A 79 " --> pdb=" O ALA K 76 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA K 78 " --> pdb=" O GLN A 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 36 hydrogen bonds defined for protein. 108 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: 0.53 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: 1.18 - 1.26: 468 1.26 - 1.33: 113 1.33 - 1.40: 355 1.40 - 1.48: 468 1.48 - 1.55: 1212 Bond restraints: 2616 Sorted by residual: bond pdb=" C7 NAG K 201 " pdb=" N2 NAG K 201 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" C7 NAG B 201 " pdb=" N2 NAG B 201 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" C7 NAG P 201 " pdb=" N2 NAG P 201 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C7 NAG H 201 " pdb=" N2 NAG H 201 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C7 NAG G 201 " pdb=" N2 NAG G 201 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.81e+01 ... (remaining 2611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 3256 1.70 - 3.40: 182 3.40 - 5.10: 96 5.10 - 6.80: 0 6.80 - 8.51: 12 Bond angle restraints: 3546 Sorted by residual: angle pdb=" CB HIS G 50 " pdb=" CG HIS G 50 " pdb=" CD2 HIS G 50 " ideal model delta sigma weight residual 131.20 122.69 8.51 1.30e+00 5.92e-01 4.28e+01 angle pdb=" CB HIS B 50 " pdb=" CG HIS B 50 " pdb=" CD2 HIS B 50 " ideal model delta sigma weight residual 131.20 122.71 8.49 1.30e+00 5.92e-01 4.27e+01 angle pdb=" CB HIS K 50 " pdb=" CG HIS K 50 " pdb=" CD2 HIS K 50 " ideal model delta sigma weight residual 131.20 122.71 8.49 1.30e+00 5.92e-01 4.26e+01 angle pdb=" CB HIS H 50 " pdb=" CG HIS H 50 " pdb=" CD2 HIS H 50 " ideal model delta sigma weight residual 131.20 122.73 8.47 1.30e+00 5.92e-01 4.24e+01 angle pdb=" CB HIS P 50 " pdb=" CG HIS P 50 " pdb=" CD2 HIS P 50 " ideal model delta sigma weight residual 131.20 122.74 8.46 1.30e+00 5.92e-01 4.24e+01 ... (remaining 3541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.32: 1320 9.32 - 18.63: 138 18.63 - 27.95: 90 27.95 - 37.26: 42 37.26 - 46.58: 12 Dihedral angle restraints: 1602 sinusoidal: 564 harmonic: 1038 Sorted by residual: dihedral pdb=" C LYS G 45 " pdb=" N LYS G 45 " pdb=" CA LYS G 45 " pdb=" CB LYS G 45 " ideal model delta harmonic sigma weight residual -122.60 -129.21 6.61 0 2.50e+00 1.60e-01 6.99e+00 dihedral pdb=" C LYS B 45 " pdb=" N LYS B 45 " pdb=" CA LYS B 45 " pdb=" CB LYS B 45 " ideal model delta harmonic sigma weight residual -122.60 -129.19 6.59 0 2.50e+00 1.60e-01 6.95e+00 dihedral pdb=" C LYS P 45 " pdb=" N LYS P 45 " pdb=" CA LYS P 45 " pdb=" CB LYS P 45 " ideal model delta harmonic sigma weight residual -122.60 -129.19 6.59 0 2.50e+00 1.60e-01 6.94e+00 ... (remaining 1599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 314 0.044 - 0.089: 101 0.089 - 0.133: 53 0.133 - 0.178: 6 0.178 - 0.222: 12 Chirality restraints: 486 Sorted by residual: chirality pdb=" CA LYS B 45 " pdb=" N LYS B 45 " pdb=" C LYS B 45 " pdb=" CB LYS B 45 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA LYS G 45 " pdb=" N LYS G 45 " pdb=" C LYS G 45 " pdb=" CB LYS G 45 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA LYS P 45 " pdb=" N LYS P 45 " pdb=" C LYS P 45 " pdb=" CB LYS P 45 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 483 not shown) Planarity restraints: 438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU G 83 " -0.004 2.00e-02 2.50e+03 8.74e-03 7.64e-01 pdb=" C GLU G 83 " 0.015 2.00e-02 2.50e+03 pdb=" O GLU G 83 " -0.006 2.00e-02 2.50e+03 pdb=" N GLY G 84 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU P 83 " -0.004 2.00e-02 2.50e+03 8.70e-03 7.56e-01 pdb=" C GLU P 83 " 0.015 2.00e-02 2.50e+03 pdb=" O GLU P 83 " -0.006 2.00e-02 2.50e+03 pdb=" N GLY P 84 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU K 83 " 0.004 2.00e-02 2.50e+03 8.57e-03 7.34e-01 pdb=" C GLU K 83 " -0.015 2.00e-02 2.50e+03 pdb=" O GLU K 83 " 0.006 2.00e-02 2.50e+03 pdb=" N GLY K 84 " 0.005 2.00e-02 2.50e+03 ... (remaining 435 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 1388 2.98 - 3.46: 2214 3.46 - 3.94: 3618 3.94 - 4.42: 4179 4.42 - 4.90: 8243 Nonbonded interactions: 19642 Sorted by model distance: nonbonded pdb=" O5 NAG B 201 " pdb=" O6 NAG B 201 " model vdw 2.505 2.432 nonbonded pdb=" O5 NAG H 201 " pdb=" O6 NAG H 201 " model vdw 2.505 2.432 nonbonded pdb=" O5 NAG G 201 " pdb=" O6 NAG G 201 " model vdw 2.505 2.432 nonbonded pdb=" O5 NAG K 201 " pdb=" O6 NAG K 201 " model vdw 2.505 2.432 nonbonded pdb=" O5 NAG P 201 " pdb=" O6 NAG P 201 " model vdw 2.506 2.432 ... (remaining 19637 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: 0.03 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'Q' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'P' } 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: 2.080 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: 0.030 Process input model: 10.870 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 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 : 0.012 0.106 2622 Z= 0.712 Angle : 2.001 39.614 3558 Z= 0.891 Chirality : 0.062 0.222 486 Planarity : 0.002 0.009 438 Dihedral : 12.572 46.580 942 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 12.82 % Favored : 87.18 % 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: -4.98 (0.27), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.20), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS K 50 TYR 0.003 0.001 TYR A 39 Details of bonding type rmsd hydrogen bonds : bond 0.18255 ( 36) hydrogen bonds : angle 7.56088 ( 108) covalent geometry : bond 0.01217 ( 2616) covalent geometry : angle 1.13106 ( 3546) link_NAG-SER : bond 0.02054 ( 6) link_NAG-SER : angle 28.43880 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.253 Fit side-chains REVERT: G 58 LYS cc_start: 0.8346 (ttmt) cc_final: 0.8080 (mtpt) REVERT: A 58 LYS cc_start: 0.8325 (ttmt) cc_final: 0.8115 (mtpt) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.2128 time to fit residues: 11.1020 Evaluate side-chains 45 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 27 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4354 r_free = 0.4354 target = 0.142782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.114777 restraints weight = 3435.398| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 3.26 r_work: 0.3925 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2622 Z= 0.090 Angle : 0.479 3.023 3558 Z= 0.247 Chirality : 0.048 0.116 486 Planarity : 0.001 0.008 438 Dihedral : 6.391 32.618 504 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.43 % Allowed : 16.24 % Favored : 83.33 % 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: -4.40 (0.30), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.23), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 TYR 0.006 0.001 TYR K 39 Details of bonding type rmsd hydrogen bonds : bond 0.01158 ( 36) hydrogen bonds : angle 4.42389 ( 108) covalent geometry : bond 0.00191 ( 2616) covalent geometry : angle 0.46034 ( 3546) link_NAG-SER : bond 0.00096 ( 6) link_NAG-SER : angle 2.32404 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.267 Fit side-chains REVERT: H 43 LYS cc_start: 0.8756 (mptt) cc_final: 0.8325 (mmtm) REVERT: B 43 LYS cc_start: 0.8817 (mptt) cc_final: 0.8425 (mtmm) REVERT: A 58 LYS cc_start: 0.8423 (ttmt) cc_final: 0.8175 (mtpt) outliers start: 1 outliers final: 1 residues processed: 44 average time/residue: 0.1862 time to fit residues: 9.4960 Evaluate side-chains 45 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 59 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 = 0.4230 r_free = 0.4230 target = 0.130895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.103836 restraints weight = 3717.465| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 3.40 r_work: 0.3752 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 2622 Z= 0.220 Angle : 0.608 4.212 3558 Z= 0.307 Chirality : 0.051 0.144 486 Planarity : 0.002 0.006 438 Dihedral : 5.212 21.715 504 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.85 % Allowed : 17.52 % Favored : 81.62 % 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: -4.15 (0.33), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.25), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS G 50 TYR 0.006 0.001 TYR P 39 Details of bonding type rmsd hydrogen bonds : bond 0.01799 ( 36) hydrogen bonds : angle 4.29906 ( 108) covalent geometry : bond 0.00476 ( 2616) covalent geometry : angle 0.58605 ( 3546) link_NAG-SER : bond 0.00585 ( 6) link_NAG-SER : angle 2.86264 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.267 Fit side-chains REVERT: H 58 LYS cc_start: 0.8352 (ttmt) cc_final: 0.8086 (mtpt) REVERT: B 43 LYS cc_start: 0.8841 (mptt) cc_final: 0.8515 (mtmm) REVERT: A 58 LYS cc_start: 0.8410 (ttmt) cc_final: 0.8202 (mtpt) outliers start: 2 outliers final: 2 residues processed: 39 average time/residue: 0.2111 time to fit residues: 9.4484 Evaluate side-chains 42 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain B residue 59 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 25 optimal weight: 0.0970 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 = 0.4275 r_free = 0.4275 target = 0.133733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.107447 restraints weight = 3591.142| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 3.27 r_work: 0.3806 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2622 Z= 0.118 Angle : 0.433 3.030 3558 Z= 0.232 Chirality : 0.048 0.132 486 Planarity : 0.001 0.006 438 Dihedral : 3.437 10.882 504 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.71 % Allowed : 18.80 % Favored : 79.49 % 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: -3.83 (0.36), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.28), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS H 50 TYR 0.004 0.001 TYR P 39 Details of bonding type rmsd hydrogen bonds : bond 0.01171 ( 36) hydrogen bonds : angle 4.15660 ( 108) covalent geometry : bond 0.00253 ( 2616) covalent geometry : angle 0.42482 ( 3546) link_NAG-SER : bond 0.00432 ( 6) link_NAG-SER : angle 1.52692 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.246 Fit side-chains REVERT: G 58 LYS cc_start: 0.8380 (ttmt) cc_final: 0.8178 (mtpt) REVERT: A 58 LYS cc_start: 0.8383 (ttmt) cc_final: 0.8180 (mtpt) outliers start: 4 outliers final: 4 residues processed: 34 average time/residue: 0.1857 time to fit residues: 7.3676 Evaluate side-chains 38 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain A residue 59 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 15 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 14 optimal weight: 0.0570 chunk 12 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 2 optimal weight: 0.4980 chunk 11 optimal weight: 4.9990 overall best weight: 2.5104 ------------------------------------------------------------------------------- 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 = 0.4240 r_free = 0.4240 target = 0.131349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.104812 restraints weight = 3667.503| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 3.34 r_work: 0.3768 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2622 Z= 0.161 Angle : 0.484 3.585 3558 Z= 0.253 Chirality : 0.049 0.129 486 Planarity : 0.001 0.005 438 Dihedral : 3.577 11.513 504 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.42 % Allowed : 20.09 % Favored : 76.50 % 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: -3.68 (0.38), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 50 TYR 0.006 0.001 TYR P 39 Details of bonding type rmsd hydrogen bonds : bond 0.01260 ( 36) hydrogen bonds : angle 4.08492 ( 108) covalent geometry : bond 0.00348 ( 2616) covalent geometry : angle 0.47460 ( 3546) link_NAG-SER : bond 0.00612 ( 6) link_NAG-SER : angle 1.70697 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.276 Fit side-chains REVERT: H 58 LYS cc_start: 0.8310 (ttmt) cc_final: 0.7978 (mtpp) REVERT: G 58 LYS cc_start: 0.8341 (ttmt) cc_final: 0.8135 (mtpt) REVERT: A 58 LYS cc_start: 0.8388 (ttmt) cc_final: 0.8182 (mtpt) outliers start: 8 outliers final: 8 residues processed: 39 average time/residue: 0.1865 time to fit residues: 8.4832 Evaluate side-chains 43 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 59 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 23 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 25 optimal weight: 0.4980 chunk 21 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 17 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- 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 = 0.4263 r_free = 0.4263 target = 0.132301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.105457 restraints weight = 3622.792| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 3.27 r_work: 0.3781 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 2622 Z= 0.166 Angle : 0.487 3.544 3558 Z= 0.257 Chirality : 0.049 0.132 486 Planarity : 0.002 0.004 438 Dihedral : 3.615 11.877 504 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.56 % Allowed : 21.79 % Favored : 72.65 % 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: -3.55 (0.39), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS H 50 TYR 0.006 0.001 TYR P 39 Details of bonding type rmsd hydrogen bonds : bond 0.01237 ( 36) hydrogen bonds : angle 3.80446 ( 108) covalent geometry : bond 0.00358 ( 2616) covalent geometry : angle 0.47890 ( 3546) link_NAG-SER : bond 0.00618 ( 6) link_NAG-SER : angle 1.60372 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.275 Fit side-chains REVERT: H 58 LYS cc_start: 0.8369 (ttmt) cc_final: 0.8070 (mtpp) outliers start: 13 outliers final: 13 residues processed: 42 average time/residue: 0.1695 time to fit residues: 8.3408 Evaluate side-chains 48 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 59 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 = 0.4250 r_free = 0.4250 target = 0.131632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.104652 restraints weight = 3686.639| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 3.29 r_work: 0.3760 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 2622 Z= 0.183 Angle : 0.508 4.265 3558 Z= 0.266 Chirality : 0.049 0.129 486 Planarity : 0.002 0.004 438 Dihedral : 3.686 12.077 504 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 5.56 % Allowed : 21.79 % Favored : 72.65 % 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: -3.49 (0.39), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 50 TYR 0.006 0.001 TYR P 39 Details of bonding type rmsd hydrogen bonds : bond 0.01286 ( 36) hydrogen bonds : angle 3.69272 ( 108) covalent geometry : bond 0.00396 ( 2616) covalent geometry : angle 0.50212 ( 3546) link_NAG-SER : bond 0.00702 ( 6) link_NAG-SER : angle 1.45756 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 32 time to evaluate : 0.272 Fit side-chains REVERT: H 58 LYS cc_start: 0.8345 (ttmt) cc_final: 0.8054 (mtpp) outliers start: 13 outliers final: 13 residues processed: 39 average time/residue: 0.1586 time to fit residues: 7.4053 Evaluate side-chains 45 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 32 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 59 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 24 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4313 r_free = 0.4313 target = 0.136372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.109436 restraints weight = 3418.104| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 3.20 r_work: 0.3841 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.008 2622 Z= 0.073 Angle : 0.368 3.967 3558 Z= 0.202 Chirality : 0.048 0.125 486 Planarity : 0.001 0.004 438 Dihedral : 3.045 10.028 504 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.85 % Allowed : 27.78 % Favored : 71.37 % 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: -3.21 (0.41), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 TYR 0.003 0.001 TYR P 39 Details of bonding type rmsd hydrogen bonds : bond 0.00852 ( 36) hydrogen bonds : angle 3.48771 ( 108) covalent geometry : bond 0.00153 ( 2616) covalent geometry : angle 0.36570 ( 3546) link_NAG-SER : bond 0.00264 ( 6) link_NAG-SER : angle 0.83755 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.245 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 34 average time/residue: 0.1651 time to fit residues: 6.6885 Evaluate side-chains 33 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain A residue 42 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 24 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.4293 r_free = 0.4293 target = 0.134929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.107749 restraints weight = 3540.285| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 3.27 r_work: 0.3812 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2622 Z= 0.107 Angle : 0.402 4.108 3558 Z= 0.215 Chirality : 0.048 0.125 486 Planarity : 0.001 0.004 438 Dihedral : 3.122 10.280 504 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.28 % Allowed : 27.35 % Favored : 71.37 % 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: -3.10 (0.41), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 50 TYR 0.005 0.001 TYR P 39 Details of bonding type rmsd hydrogen bonds : bond 0.00924 ( 36) hydrogen bonds : angle 3.44660 ( 108) covalent geometry : bond 0.00233 ( 2616) covalent geometry : angle 0.39770 ( 3546) link_NAG-SER : bond 0.00450 ( 6) link_NAG-SER : angle 1.06583 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.274 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 32 average time/residue: 0.1821 time to fit residues: 6.9213 Evaluate side-chains 33 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 59 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 19 optimal weight: 0.0970 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 = 0.4271 r_free = 0.4271 target = 0.133416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.106241 restraints weight = 3555.495| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 3.28 r_work: 0.3787 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2622 Z= 0.143 Angle : 0.444 4.256 3558 Z= 0.235 Chirality : 0.048 0.126 486 Planarity : 0.001 0.004 438 Dihedral : 3.358 11.144 504 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.14 % Allowed : 26.50 % Favored : 71.37 % 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: -3.09 (0.41), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 50 TYR 0.006 0.001 TYR P 39 Details of bonding type rmsd hydrogen bonds : bond 0.01047 ( 36) hydrogen bonds : angle 3.48301 ( 108) covalent geometry : bond 0.00309 ( 2616) covalent geometry : angle 0.43856 ( 3546) link_NAG-SER : bond 0.00559 ( 6) link_NAG-SER : angle 1.27239 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.291 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 33 average time/residue: 0.1667 time to fit residues: 6.6214 Evaluate side-chains 36 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain A residue 59 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 23 optimal weight: 0.0980 chunk 26 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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 = 0.4282 r_free = 0.4282 target = 0.133998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.106983 restraints weight = 3477.303| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 3.22 r_work: 0.3807 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 2622 Z= 0.125 Angle : 0.413 4.064 3558 Z= 0.222 Chirality : 0.048 0.123 486 Planarity : 0.001 0.004 438 Dihedral : 3.189 10.712 504 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.56 % Allowed : 26.50 % Favored : 70.94 % 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: -3.00 (0.42), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 TYR 0.005 0.001 TYR P 39 Details of bonding type rmsd hydrogen bonds : bond 0.00983 ( 36) hydrogen bonds : angle 3.43384 ( 108) covalent geometry : bond 0.00271 ( 2616) covalent geometry : angle 0.40944 ( 3546) link_NAG-SER : bond 0.00519 ( 6) link_NAG-SER : angle 1.06874 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1519.57 seconds wall clock time: 27 minutes 22.51 seconds (1642.51 seconds total)