Starting phenix.real_space_refine on Fri May 9 15:52:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jaz_61302/05_2025/9jaz_61302.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jaz_61302/05_2025/9jaz_61302.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jaz_61302/05_2025/9jaz_61302.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jaz_61302/05_2025/9jaz_61302.map" model { file = "/net/cci-nas-00/data/ceres_data/9jaz_61302/05_2025/9jaz_61302.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jaz_61302/05_2025/9jaz_61302.cif" } resolution = 3.0 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 1956 2.51 5 N 504 2.21 5 O 540 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: 3012 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 121 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "A" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 130 Classifications: {'peptide': 20} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 19} Restraints were copied for chains: AA, C, B, E, D, BB, F, EE, DD, CC, FF Time building chain proxies: 1.49, per 1000 atoms: 0.49 Number of scatterers: 3012 At special positions: 0 Unit cell: (68.89, 73.87, 44.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 540 8.00 N 504 7.00 C 1956 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 TRANS " DAS A 23 " - " GLU A 22 " " DAS B 23 " - " GLU B 22 " " DAS C 23 " - " GLU C 22 " " DAS D 23 " - " GLU D 22 " " DAS E 23 " - " GLU E 22 " " DAS F 23 " - " GLU F 22 " " DASAA 23 " - " GLUAA 22 " " DASBB 23 " - " GLUBB 22 " " DASCC 23 " - " GLUCC 22 " " DASDD 23 " - " GLUDD 22 " " DASEE 23 " - " GLUEE 22 " " DASFF 23 " - " GLUFF 22 " Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 369.4 milliseconds 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAS F 23 " pdb=" CB DAS E 23 " pdb=" CB DAS D 23 " pdb=" CB DAS C 23 " pdb=" CB DAS B 23 " pdb=" CB DAS A 23 " pdb=" CB DASFF 23 " pdb=" CB DASEE 23 " pdb=" CB DASDD 23 " pdb=" CB DASCC 23 " pdb=" CB DASBB 23 " pdb=" CB DASAA 23 " Number of C-beta restraints generated: 648 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 42.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'F' and resid 10 through 13 Processing sheet with id=AA2, first strand: chain 'F' and resid 15 through 20 Processing sheet with id=AA3, first strand: chain 'F' and resid 30 through 32 removed outlier: 6.674A pdb=" N ALA F 30 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA E 30 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA D 30 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA C 30 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA B 30 " --> pdb=" O ILE A 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'F' and resid 34 through 36 removed outlier: 8.983A pdb=" N LEU F 34 " --> pdb=" O MET E 35 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N LEU E 34 " --> pdb=" O MET D 35 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N LEU D 34 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 9.005A pdb=" N LEU C 34 " --> pdb=" O MET B 35 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N LEU B 34 " --> pdb=" O MET A 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 39 through 41 removed outlier: 6.082A pdb=" N VAL F 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL E 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N VAL D 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL C 39 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N VAL B 39 " --> pdb=" O VAL A 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'FF' and resid 10 through 13 Processing sheet with id=AA7, first strand: chain 'FF' and resid 15 through 20 Processing sheet with id=AA8, first strand: chain 'FF' and resid 30 through 32 removed outlier: 6.642A pdb=" N ALAFF 30 " --> pdb=" O ILEEE 31 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALAEE 30 " --> pdb=" O ILEDD 31 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALADD 30 " --> pdb=" O ILECC 31 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALACC 30 " --> pdb=" O ILEBB 31 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALABB 30 " --> pdb=" O ILEAA 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'FF' and resid 34 through 36 removed outlier: 9.004A pdb=" N LEUFF 34 " --> pdb=" O METEE 35 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N LEUEE 34 " --> pdb=" O METDD 35 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N LEUDD 34 " --> pdb=" O METCC 35 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N LEUCC 34 " --> pdb=" O METBB 35 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N LEUBB 34 " --> pdb=" O METAA 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AA10, first strand: chain 'FF' and resid 39 through 41 removed outlier: 6.121A pdb=" N VALFF 39 " --> pdb=" O VALEE 40 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VALEE 39 " --> pdb=" O VALDD 40 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VALDD 39 " --> pdb=" O VALCC 40 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VALCC 39 " --> pdb=" O VALBB 40 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VALBB 39 " --> pdb=" O VALAA 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA10 80 hydrogen bonds defined for protein. 240 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: 0.67 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 972 1.34 - 1.45: 384 1.45 - 1.57: 1668 1.57 - 1.68: 0 1.68 - 1.79: 24 Bond restraints: 3048 Sorted by residual: bond pdb=" C VALFF 36 " pdb=" N GLYFF 37 " ideal model delta sigma weight residual 1.327 1.320 0.007 1.11e-02 8.12e+03 3.86e-01 bond pdb=" C VAL F 36 " pdb=" N GLY F 37 " ideal model delta sigma weight residual 1.327 1.320 0.007 1.11e-02 8.12e+03 3.70e-01 bond pdb=" C VALEE 36 " pdb=" N GLYEE 37 " ideal model delta sigma weight residual 1.327 1.320 0.007 1.11e-02 8.12e+03 3.49e-01 bond pdb=" C VALDD 36 " pdb=" N GLYDD 37 " ideal model delta sigma weight residual 1.327 1.320 0.007 1.11e-02 8.12e+03 3.47e-01 bond pdb=" C VALCC 36 " pdb=" N GLYCC 37 " ideal model delta sigma weight residual 1.327 1.320 0.006 1.11e-02 8.12e+03 3.34e-01 ... (remaining 3043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.62: 3492 0.62 - 1.25: 430 1.25 - 1.87: 98 1.87 - 2.50: 36 2.50 - 3.12: 24 Bond angle restraints: 4080 Sorted by residual: angle pdb=" C SER D 26 " pdb=" CA SER D 26 " pdb=" CB SER D 26 " ideal model delta sigma weight residual 111.89 109.85 2.04 1.42e+00 4.96e-01 2.06e+00 angle pdb=" C SERBB 26 " pdb=" CA SERBB 26 " pdb=" CB SERBB 26 " ideal model delta sigma weight residual 111.89 109.85 2.04 1.42e+00 4.96e-01 2.06e+00 angle pdb=" C SER C 26 " pdb=" CA SER C 26 " pdb=" CB SER C 26 " ideal model delta sigma weight residual 111.89 109.86 2.03 1.42e+00 4.96e-01 2.05e+00 angle pdb=" N GLYAA 25 " pdb=" CA GLYAA 25 " pdb=" C GLYAA 25 " ideal model delta sigma weight residual 111.31 114.08 -2.77 1.95e+00 2.63e-01 2.02e+00 angle pdb=" N GLYDD 25 " pdb=" CA GLYDD 25 " pdb=" C GLYDD 25 " ideal model delta sigma weight residual 111.31 114.07 -2.76 1.95e+00 2.63e-01 2.01e+00 ... (remaining 4075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.28: 1381 11.28 - 22.55: 155 22.55 - 33.83: 96 33.83 - 45.10: 48 45.10 - 56.37: 24 Dihedral angle restraints: 1704 sinusoidal: 648 harmonic: 1056 Sorted by residual: dihedral pdb=" CA LEUAA 17 " pdb=" CB LEUAA 17 " pdb=" CG LEUAA 17 " pdb=" CD1 LEUAA 17 " ideal model delta sinusoidal sigma weight residual 180.00 138.50 41.50 3 1.50e+01 4.44e-03 7.43e+00 dihedral pdb=" CA LEUFF 17 " pdb=" CB LEUFF 17 " pdb=" CG LEUFF 17 " pdb=" CD1 LEUFF 17 " ideal model delta sinusoidal sigma weight residual 180.00 138.51 41.49 3 1.50e+01 4.44e-03 7.42e+00 dihedral pdb=" CA LEU A 17 " pdb=" CB LEU A 17 " pdb=" CG LEU A 17 " pdb=" CD1 LEU A 17 " ideal model delta sinusoidal sigma weight residual 180.00 138.51 41.49 3 1.50e+01 4.44e-03 7.42e+00 ... (remaining 1701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 216 0.026 - 0.051: 134 0.051 - 0.076: 22 0.076 - 0.102: 32 0.102 - 0.127: 64 Chirality restraints: 468 Sorted by residual: chirality pdb=" CA VALEE 12 " pdb=" N VALEE 12 " pdb=" C VALEE 12 " pdb=" CB VALEE 12 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.05e-01 chirality pdb=" CA VAL D 12 " pdb=" N VAL D 12 " pdb=" C VAL D 12 " pdb=" CB VAL D 12 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.05e-01 chirality pdb=" CA VAL F 12 " pdb=" N VAL F 12 " pdb=" C VAL F 12 " pdb=" CB VAL F 12 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 465 not shown) Planarity restraints: 528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS F 13 " -0.003 2.00e-02 2.50e+03 5.43e-03 2.95e-01 pdb=" C HIS F 13 " 0.009 2.00e-02 2.50e+03 pdb=" O HIS F 13 " -0.004 2.00e-02 2.50e+03 pdb=" N HIS F 14 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 13 " -0.003 2.00e-02 2.50e+03 5.41e-03 2.93e-01 pdb=" C HIS A 13 " 0.009 2.00e-02 2.50e+03 pdb=" O HIS A 13 " -0.004 2.00e-02 2.50e+03 pdb=" N HIS A 14 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HISFF 13 " 0.003 2.00e-02 2.50e+03 5.34e-03 2.86e-01 pdb=" C HISFF 13 " -0.009 2.00e-02 2.50e+03 pdb=" O HISFF 13 " 0.004 2.00e-02 2.50e+03 pdb=" N HISFF 14 " 0.003 2.00e-02 2.50e+03 ... (remaining 525 not shown) Histogram of nonbonded interaction distances: 2.62 - 3.08: 1949 3.08 - 3.53: 2807 3.53 - 3.99: 4789 3.99 - 4.44: 5730 4.44 - 4.90: 10681 Nonbonded interactions: 25956 Sorted by model distance: nonbonded pdb=" O DASEE 23 " pdb=" N VALDD 24 " model vdw 2.622 3.120 nonbonded pdb=" O DASBB 23 " pdb=" N VALAA 24 " model vdw 2.636 3.120 nonbonded pdb=" O DAS E 23 " pdb=" N VAL D 24 " model vdw 2.649 3.120 nonbonded pdb=" O DAS F 23 " pdb=" N VAL E 24 " model vdw 2.649 3.120 nonbonded pdb=" O DASFF 23 " pdb=" N VALEE 24 " model vdw 2.660 3.120 ... (remaining 25951 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 'A' selection = chain 'AA' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'BB' selection = chain 'F' selection = chain 'EE' selection = chain 'DD' selection = chain 'CC' selection = chain 'FF' } 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: 0.700 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: 0.030 Process input model: 10.920 Find NCS groups from input model: 0.070 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:10.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 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 0.019 3060 Z= 0.168 Angle : 0.522 3.123 4116 Z= 0.309 Chirality : 0.054 0.127 468 Planarity : 0.001 0.005 516 Dihedral : 15.936 56.374 1020 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 33.33 % Favored : 66.67 % 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: -0.70 (0.44), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.53 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS C 13 PHE 0.007 0.002 PHE B 20 TYR 0.003 0.001 TYR C 10 Details of bonding type rmsd link_TRANS : bond 0.00097 ( 12) link_TRANS : angle 0.12721 ( 36) hydrogen bonds : bond 0.13977 ( 80) hydrogen bonds : angle 8.03712 ( 240) covalent geometry : bond 0.00378 ( 3048) covalent geometry : angle 0.52464 ( 4080) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.294 Fit side-chains REVERT: D 28 LYS cc_start: 0.8573 (mtpm) cc_final: 0.8161 (mttp) REVERT: C 28 LYS cc_start: 0.8500 (mtpm) cc_final: 0.8093 (mttp) REVERT: B 28 LYS cc_start: 0.8506 (mtpm) cc_final: 0.8019 (mttp) REVERT: A 28 LYS cc_start: 0.8891 (mtpm) cc_final: 0.8508 (mttm) REVERT: EE 28 LYS cc_start: 0.8628 (mtpm) cc_final: 0.8393 (mtpt) REVERT: DD 28 LYS cc_start: 0.8526 (mtpm) cc_final: 0.8158 (mttm) REVERT: CC 28 LYS cc_start: 0.8483 (mtpm) cc_final: 0.8104 (mttp) REVERT: BB 28 LYS cc_start: 0.8374 (mtpm) cc_final: 0.7866 (mttp) REVERT: AA 28 LYS cc_start: 0.8861 (mtpm) cc_final: 0.8421 (mttp) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 1.8775 time to fit residues: 46.1262 Evaluate side-chains 24 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.115746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.080456 restraints weight = 3357.194| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.95 r_work: 0.3212 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 3060 Z= 0.196 Angle : 0.496 4.959 4116 Z= 0.279 Chirality : 0.058 0.129 468 Planarity : 0.002 0.007 516 Dihedral : 4.937 14.522 432 Min Nonbonded Distance : 2.694 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.74 % Allowed : 31.94 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.45), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.57 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 13 PHE 0.011 0.002 PHE A 20 TYR 0.003 0.001 TYR F 10 Details of bonding type rmsd link_TRANS : bond 0.00083 ( 12) link_TRANS : angle 0.18810 ( 36) hydrogen bonds : bond 0.03873 ( 80) hydrogen bonds : angle 5.02794 ( 240) covalent geometry : bond 0.00477 ( 3048) covalent geometry : angle 0.49825 ( 4080) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.289 Fit side-chains REVERT: D 28 LYS cc_start: 0.8135 (mtpm) cc_final: 0.7679 (mttp) REVERT: C 28 LYS cc_start: 0.8175 (mtpm) cc_final: 0.7675 (mttp) REVERT: B 28 LYS cc_start: 0.8275 (mtpm) cc_final: 0.7719 (mttp) REVERT: A 28 LYS cc_start: 0.8683 (mtpm) cc_final: 0.8243 (mttm) REVERT: DD 28 LYS cc_start: 0.8080 (mtpm) cc_final: 0.7591 (mttm) REVERT: CC 28 LYS cc_start: 0.8102 (mtpm) cc_final: 0.7667 (mttp) REVERT: CC 35 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8112 (ttt) REVERT: BB 28 LYS cc_start: 0.8117 (mtpm) cc_final: 0.7550 (mttp) REVERT: AA 28 LYS cc_start: 0.8605 (mtpm) cc_final: 0.7979 (mttp) outliers start: 5 outliers final: 3 residues processed: 24 average time/residue: 1.7605 time to fit residues: 43.2988 Evaluate side-chains 28 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain DD residue 35 MET Chi-restraints excluded: chain CC residue 35 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.112926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.077794 restraints weight = 3365.178| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.98 r_work: 0.3084 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.054 3060 Z= 0.408 Angle : 0.653 4.969 4116 Z= 0.369 Chirality : 0.063 0.139 468 Planarity : 0.003 0.009 516 Dihedral : 5.881 22.881 432 Min Nonbonded Distance : 2.674 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 6.60 % Allowed : 26.39 % Favored : 67.01 % 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 (0.45), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.56 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS E 13 PHE 0.017 0.003 PHE C 19 TYR 0.007 0.001 TYR E 10 Details of bonding type rmsd link_TRANS : bond 0.00239 ( 12) link_TRANS : angle 0.34079 ( 36) hydrogen bonds : bond 0.04068 ( 80) hydrogen bonds : angle 4.82914 ( 240) covalent geometry : bond 0.00978 ( 3048) covalent geometry : angle 0.65520 ( 4080) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 24 time to evaluate : 0.285 Fit side-chains REVERT: D 28 LYS cc_start: 0.8245 (mtpm) cc_final: 0.7765 (mttp) REVERT: C 28 LYS cc_start: 0.8289 (mtpm) cc_final: 0.7795 (mttp) REVERT: B 28 LYS cc_start: 0.8340 (mtpm) cc_final: 0.7783 (mttp) REVERT: A 28 LYS cc_start: 0.8698 (mtpm) cc_final: 0.8198 (mttm) REVERT: FF 35 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7517 (ttm) REVERT: DD 28 LYS cc_start: 0.8087 (mtpm) cc_final: 0.7623 (mttp) REVERT: CC 28 LYS cc_start: 0.8114 (mtpm) cc_final: 0.7618 (mttp) REVERT: BB 28 LYS cc_start: 0.8253 (mtpm) cc_final: 0.7673 (mttp) REVERT: BB 35 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8182 (ttt) REVERT: AA 28 LYS cc_start: 0.8689 (mtpm) cc_final: 0.8154 (mttp) outliers start: 19 outliers final: 5 residues processed: 37 average time/residue: 1.3292 time to fit residues: 50.5969 Evaluate side-chains 31 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain FF residue 35 MET Chi-restraints excluded: chain DD residue 35 MET Chi-restraints excluded: chain DD residue 39 VAL Chi-restraints excluded: chain BB residue 35 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 0.3980 chunk 25 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3915 r_free = 0.3915 target = 0.117864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.082526 restraints weight = 3437.748| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 3.02 r_work: 0.3210 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3060 Z= 0.137 Angle : 0.456 5.197 4116 Z= 0.259 Chirality : 0.058 0.123 468 Planarity : 0.002 0.007 516 Dihedral : 5.094 18.282 432 Min Nonbonded Distance : 2.696 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.82 % Allowed : 27.78 % Favored : 68.40 % 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 (0.44), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.60 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HISDD 13 PHE 0.008 0.002 PHE C 19 TYR 0.003 0.001 TYR D 10 Details of bonding type rmsd link_TRANS : bond 0.00039 ( 12) link_TRANS : angle 0.22821 ( 36) hydrogen bonds : bond 0.02862 ( 80) hydrogen bonds : angle 4.70791 ( 240) covalent geometry : bond 0.00328 ( 3048) covalent geometry : angle 0.45801 ( 4080) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 24 time to evaluate : 0.292 Fit side-chains REVERT: D 28 LYS cc_start: 0.8252 (mtpm) cc_final: 0.7787 (mttp) REVERT: C 28 LYS cc_start: 0.8236 (mtpm) cc_final: 0.7728 (mttp) REVERT: B 28 LYS cc_start: 0.8382 (mtpm) cc_final: 0.7842 (mttp) REVERT: A 28 LYS cc_start: 0.8748 (mtpm) cc_final: 0.8333 (mttp) REVERT: FF 35 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.7342 (ttm) REVERT: DD 28 LYS cc_start: 0.8193 (mtpm) cc_final: 0.7741 (mttp) REVERT: CC 28 LYS cc_start: 0.8161 (mtpm) cc_final: 0.7727 (mttp) REVERT: BB 28 LYS cc_start: 0.8296 (mtpm) cc_final: 0.7706 (mttp) REVERT: AA 28 LYS cc_start: 0.8631 (mtpm) cc_final: 0.8022 (mttp) outliers start: 11 outliers final: 0 residues processed: 29 average time/residue: 1.5191 time to fit residues: 45.2225 Evaluate side-chains 25 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain FF residue 35 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 4 optimal weight: 5.9990 chunk 10 optimal weight: 0.0470 chunk 24 optimal weight: 0.8980 chunk 34 optimal weight: 0.0060 chunk 5 optimal weight: 0.6980 overall best weight: 0.4494 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.120656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.085133 restraints weight = 3410.137| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 3.00 r_work: 0.3253 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3060 Z= 0.109 Angle : 0.432 5.297 4116 Z= 0.244 Chirality : 0.057 0.121 468 Planarity : 0.002 0.007 516 Dihedral : 4.798 16.190 432 Min Nonbonded Distance : 2.694 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.82 % Allowed : 28.47 % Favored : 67.71 % 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 (0.44), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.61 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HISDD 13 PHE 0.007 0.002 PHE A 20 TYR 0.003 0.001 TYR D 10 Details of bonding type rmsd link_TRANS : bond 0.00028 ( 12) link_TRANS : angle 0.28475 ( 36) hydrogen bonds : bond 0.02738 ( 80) hydrogen bonds : angle 4.62257 ( 240) covalent geometry : bond 0.00261 ( 3048) covalent geometry : angle 0.43336 ( 4080) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 24 time to evaluate : 0.323 Fit side-chains REVERT: D 17 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8121 (tt) REVERT: D 28 LYS cc_start: 0.8229 (mtpm) cc_final: 0.7752 (mttp) REVERT: C 28 LYS cc_start: 0.8206 (mtpm) cc_final: 0.7708 (mttp) REVERT: B 28 LYS cc_start: 0.8352 (mtpm) cc_final: 0.7805 (mttp) REVERT: A 28 LYS cc_start: 0.8622 (mtpm) cc_final: 0.8238 (mttm) REVERT: FF 35 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7286 (ttm) REVERT: DD 28 LYS cc_start: 0.8178 (mtpm) cc_final: 0.7716 (mttp) REVERT: CC 17 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.8019 (tt) REVERT: CC 28 LYS cc_start: 0.8084 (mtpm) cc_final: 0.7631 (mttp) REVERT: BB 28 LYS cc_start: 0.8220 (mtpm) cc_final: 0.7700 (mtmm) REVERT: AA 28 LYS cc_start: 0.8566 (mtpm) cc_final: 0.8138 (mttp) outliers start: 11 outliers final: 1 residues processed: 28 average time/residue: 1.5696 time to fit residues: 45.1010 Evaluate side-chains 28 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain FF residue 35 MET Chi-restraints excluded: chain DD residue 35 MET Chi-restraints excluded: chain CC residue 17 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3792 r_free = 0.3792 target = 0.111635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.076026 restraints weight = 3561.104| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 3.07 r_work: 0.3069 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.070 3060 Z= 0.500 Angle : 0.741 5.658 4116 Z= 0.411 Chirality : 0.064 0.138 468 Planarity : 0.003 0.011 516 Dihedral : 6.028 23.784 432 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 6.25 % Allowed : 26.74 % Favored : 67.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.44), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.57 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HISDD 13 PHE 0.021 0.004 PHE C 19 TYR 0.009 0.001 TYR F 10 Details of bonding type rmsd link_TRANS : bond 0.00307 ( 12) link_TRANS : angle 0.31685 ( 36) hydrogen bonds : bond 0.03801 ( 80) hydrogen bonds : angle 4.67535 ( 240) covalent geometry : bond 0.01196 ( 3048) covalent geometry : angle 0.74415 ( 4080) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 24 time to evaluate : 0.309 Fit side-chains REVERT: D 17 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8090 (tt) REVERT: D 28 LYS cc_start: 0.8264 (mtpm) cc_final: 0.7765 (mttp) REVERT: D 35 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8293 (ttp) REVERT: C 28 LYS cc_start: 0.8264 (mtpm) cc_final: 0.7841 (mttp) REVERT: B 28 LYS cc_start: 0.8419 (mtpm) cc_final: 0.7864 (mttp) REVERT: B 35 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8568 (ttt) REVERT: A 28 LYS cc_start: 0.8747 (mtpm) cc_final: 0.8300 (mttm) REVERT: FF 35 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7465 (ttm) REVERT: DD 28 LYS cc_start: 0.8195 (mtpm) cc_final: 0.7722 (mttp) REVERT: CC 17 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8083 (tt) REVERT: CC 28 LYS cc_start: 0.8176 (mtpm) cc_final: 0.7743 (mttp) REVERT: CC 35 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8300 (ttt) REVERT: BB 28 LYS cc_start: 0.8284 (mtpm) cc_final: 0.7705 (mttp) REVERT: AA 28 LYS cc_start: 0.8715 (mtpm) cc_final: 0.8220 (mttp) outliers start: 18 outliers final: 4 residues processed: 33 average time/residue: 1.4152 time to fit residues: 48.0345 Evaluate side-chains 34 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 24 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain FF residue 35 MET Chi-restraints excluded: chain DD residue 35 MET Chi-restraints excluded: chain DD residue 39 VAL Chi-restraints excluded: chain CC residue 17 LEU Chi-restraints excluded: chain CC residue 35 MET Chi-restraints excluded: chain CC residue 39 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 27 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 4 optimal weight: 0.2980 chunk 7 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.117864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.082591 restraints weight = 3321.297| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.99 r_work: 0.3232 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3060 Z= 0.142 Angle : 0.481 5.750 4116 Z= 0.267 Chirality : 0.058 0.128 468 Planarity : 0.002 0.007 516 Dihedral : 5.255 21.492 432 Min Nonbonded Distance : 2.696 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.12 % Allowed : 29.17 % Favored : 67.71 % 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 (0.43), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.60 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HISDD 13 PHE 0.008 0.002 PHE D 20 TYR 0.003 0.001 TYR D 10 Details of bonding type rmsd link_TRANS : bond 0.00044 ( 12) link_TRANS : angle 0.28235 ( 36) hydrogen bonds : bond 0.02849 ( 80) hydrogen bonds : angle 4.66474 ( 240) covalent geometry : bond 0.00341 ( 3048) covalent geometry : angle 0.48242 ( 4080) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.288 Fit side-chains REVERT: D 17 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8121 (tt) REVERT: D 28 LYS cc_start: 0.8230 (mtpm) cc_final: 0.7751 (mttp) REVERT: C 28 LYS cc_start: 0.8196 (mtpm) cc_final: 0.7736 (mttp) REVERT: B 28 LYS cc_start: 0.8355 (mtpm) cc_final: 0.7786 (mttp) REVERT: A 28 LYS cc_start: 0.8672 (mtpm) cc_final: 0.8255 (mttp) REVERT: FF 35 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7331 (ttm) REVERT: DD 28 LYS cc_start: 0.8160 (mtpm) cc_final: 0.7693 (mttp) REVERT: CC 17 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8056 (tt) REVERT: CC 28 LYS cc_start: 0.8081 (mtpm) cc_final: 0.7649 (mttp) REVERT: BB 28 LYS cc_start: 0.8266 (mtpm) cc_final: 0.7742 (mtmm) REVERT: AA 28 LYS cc_start: 0.8598 (mtpm) cc_final: 0.7999 (mttp) outliers start: 9 outliers final: 0 residues processed: 27 average time/residue: 1.6751 time to fit residues: 46.3688 Evaluate side-chains 27 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain FF residue 35 MET Chi-restraints excluded: chain CC residue 17 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3838 r_free = 0.3838 target = 0.113139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.077651 restraints weight = 3416.656| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.03 r_work: 0.3137 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 3060 Z= 0.309 Angle : 0.597 6.137 4116 Z= 0.333 Chirality : 0.060 0.131 468 Planarity : 0.003 0.008 516 Dihedral : 5.615 22.257 432 Min Nonbonded Distance : 2.675 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.51 % Allowed : 27.43 % Favored : 68.06 % 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: -0.82 (0.44), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.62 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS D 13 PHE 0.015 0.003 PHE C 19 TYR 0.005 0.001 TYR E 10 Details of bonding type rmsd link_TRANS : bond 0.00132 ( 12) link_TRANS : angle 0.17557 ( 36) hydrogen bonds : bond 0.03355 ( 80) hydrogen bonds : angle 4.64348 ( 240) covalent geometry : bond 0.00742 ( 3048) covalent geometry : angle 0.59957 ( 4080) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 24 time to evaluate : 0.288 Fit side-chains REVERT: D 17 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8120 (tt) REVERT: D 28 LYS cc_start: 0.8250 (mtpm) cc_final: 0.7757 (mttp) REVERT: C 28 LYS cc_start: 0.8303 (mtpm) cc_final: 0.7846 (mttp) REVERT: B 28 LYS cc_start: 0.8398 (mtpm) cc_final: 0.7830 (mttp) REVERT: A 28 LYS cc_start: 0.8769 (mtpm) cc_final: 0.8354 (mttp) REVERT: FF 35 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7541 (ttm) REVERT: DD 28 LYS cc_start: 0.8192 (mtpm) cc_final: 0.7723 (mttp) REVERT: CC 17 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8134 (tt) REVERT: CC 28 LYS cc_start: 0.8159 (mtpm) cc_final: 0.7721 (mttp) REVERT: BB 28 LYS cc_start: 0.8313 (mtpm) cc_final: 0.7822 (mtmm) REVERT: AA 28 LYS cc_start: 0.8716 (mtpm) cc_final: 0.8209 (mttp) outliers start: 13 outliers final: 3 residues processed: 30 average time/residue: 1.4547 time to fit residues: 44.8908 Evaluate side-chains 30 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain FF residue 35 MET Chi-restraints excluded: chain CC residue 17 LEU Chi-restraints excluded: chain CC residue 39 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 9 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 12 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 0.0980 chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.5382 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.120695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.085364 restraints weight = 3335.308| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.97 r_work: 0.3257 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3060 Z= 0.125 Angle : 0.462 5.985 4116 Z= 0.258 Chirality : 0.058 0.128 468 Planarity : 0.002 0.007 516 Dihedral : 5.054 20.645 432 Min Nonbonded Distance : 2.695 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.78 % Allowed : 29.17 % Favored : 68.06 % 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: -0.79 (0.44), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.59 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HISDD 13 PHE 0.008 0.002 PHE D 20 TYR 0.004 0.001 TYRDD 10 Details of bonding type rmsd link_TRANS : bond 0.00028 ( 12) link_TRANS : angle 0.33925 ( 36) hydrogen bonds : bond 0.02762 ( 80) hydrogen bonds : angle 4.63042 ( 240) covalent geometry : bond 0.00299 ( 3048) covalent geometry : angle 0.46342 ( 4080) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.307 Fit side-chains REVERT: D 17 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8104 (tt) REVERT: D 28 LYS cc_start: 0.8224 (mtpm) cc_final: 0.7738 (mttp) REVERT: C 28 LYS cc_start: 0.8176 (mtpm) cc_final: 0.7698 (mttp) REVERT: B 28 LYS cc_start: 0.8329 (mtpm) cc_final: 0.7772 (mttp) REVERT: A 28 LYS cc_start: 0.8642 (mtpm) cc_final: 0.8242 (mttm) REVERT: FF 35 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.7235 (ttm) REVERT: DD 28 LYS cc_start: 0.8138 (mtpm) cc_final: 0.7673 (mttp) REVERT: CC 17 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8053 (tt) REVERT: CC 28 LYS cc_start: 0.8044 (mtpm) cc_final: 0.7609 (mttp) REVERT: BB 28 LYS cc_start: 0.8224 (mtpm) cc_final: 0.7620 (mttp) REVERT: AA 28 LYS cc_start: 0.8601 (mtpm) cc_final: 0.8176 (mttp) outliers start: 8 outliers final: 0 residues processed: 27 average time/residue: 1.5916 time to fit residues: 44.1318 Evaluate side-chains 27 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain FF residue 35 MET Chi-restraints excluded: chain CC residue 17 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 2 optimal weight: 0.0470 overall best weight: 0.9682 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.118277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.082776 restraints weight = 3281.156| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.98 r_work: 0.3216 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3060 Z= 0.189 Angle : 0.506 6.046 4116 Z= 0.283 Chirality : 0.058 0.124 468 Planarity : 0.002 0.007 516 Dihedral : 5.185 20.731 432 Min Nonbonded Distance : 2.692 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.39 % Allowed : 31.25 % Favored : 67.36 % 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 (0.44), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.58 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HISDD 13 PHE 0.011 0.003 PHE A 20 TYR 0.004 0.001 TYRDD 10 Details of bonding type rmsd link_TRANS : bond 0.00045 ( 12) link_TRANS : angle 0.25221 ( 36) hydrogen bonds : bond 0.03060 ( 80) hydrogen bonds : angle 4.63774 ( 240) covalent geometry : bond 0.00455 ( 3048) covalent geometry : angle 0.50809 ( 4080) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.326 Fit side-chains REVERT: D 17 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8137 (tt) REVERT: D 28 LYS cc_start: 0.8292 (mtpm) cc_final: 0.7808 (mttp) REVERT: C 28 LYS cc_start: 0.8270 (mtpm) cc_final: 0.7802 (mttp) REVERT: B 28 LYS cc_start: 0.8409 (mtpm) cc_final: 0.7840 (mttp) REVERT: A 28 LYS cc_start: 0.8717 (mtpm) cc_final: 0.8318 (mttp) REVERT: FF 35 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.7258 (ttm) REVERT: DD 28 LYS cc_start: 0.8213 (mtpm) cc_final: 0.7749 (mttp) REVERT: CC 17 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8128 (tt) REVERT: CC 28 LYS cc_start: 0.8142 (mtpm) cc_final: 0.7711 (mttp) REVERT: BB 28 LYS cc_start: 0.8281 (mtpm) cc_final: 0.7792 (mtmm) REVERT: AA 28 LYS cc_start: 0.8701 (mtpm) cc_final: 0.8117 (mttp) outliers start: 4 outliers final: 0 residues processed: 26 average time/residue: 1.7547 time to fit residues: 46.7638 Evaluate side-chains 27 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain FF residue 35 MET Chi-restraints excluded: chain CC residue 17 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 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 = 0.3878 r_free = 0.3878 target = 0.116787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.081263 restraints weight = 3312.174| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 3.01 r_work: 0.3191 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 3060 Z= 0.238 Angle : 0.540 6.095 4116 Z= 0.303 Chirality : 0.059 0.127 468 Planarity : 0.002 0.007 516 Dihedral : 5.378 21.542 432 Min Nonbonded Distance : 2.681 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.43 % Allowed : 30.56 % Favored : 67.01 % 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: -0.78 (0.44), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.58 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS D 13 PHE 0.013 0.003 PHE A 20 TYR 0.005 0.001 TYR E 10 Details of bonding type rmsd link_TRANS : bond 0.00080 ( 12) link_TRANS : angle 0.20695 ( 36) hydrogen bonds : bond 0.03182 ( 80) hydrogen bonds : angle 4.64151 ( 240) covalent geometry : bond 0.00575 ( 3048) covalent geometry : angle 0.54238 ( 4080) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2258.11 seconds wall clock time: 39 minutes 39.11 seconds (2379.11 seconds total)