Starting phenix.real_space_refine on Tue Mar 3 11:06:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vzf_32227/03_2026/7vzf_32227.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vzf_32227/03_2026/7vzf_32227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vzf_32227/03_2026/7vzf_32227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vzf_32227/03_2026/7vzf_32227.map" model { file = "/net/cci-nas-00/data/ceres_data/7vzf_32227/03_2026/7vzf_32227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vzf_32227/03_2026/7vzf_32227.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } 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: 4 Type Number sf(0) Gaussians S 9 5.16 5 C 1617 2.51 5 N 468 2.21 5 O 534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2628 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 876 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain breaks: 1 Restraints were copied for chains: B, C Time building chain proxies: 0.57, per 1000 atoms: 0.22 Number of scatterers: 2628 At special positions: 0 Unit cell: (98.8, 100.88, 37.44, 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 9 16.00 O 534 8.00 N 468 7.00 C 1617 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 Time building additional restraints: 0.19 Conformation dependent library (CDL) restraints added in 105.2 milliseconds 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 612 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 8 removed outlier: 6.689A pdb=" N VAL A 7 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B 7 " --> pdb=" O LEU C 8 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 18 Processing sheet with id=AA3, first strand: chain 'A' and resid 23 through 25 Processing sheet with id=AA4, first strand: chain 'A' and resid 32 through 41 removed outlier: 7.107A pdb=" N GLY B 33 " --> pdb=" O TRP A 32 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N SER A 34 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE B 35 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LYS A 36 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLY B 37 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLY C 33 " --> pdb=" O TRP B 32 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER B 34 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE C 35 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS B 36 " --> pdb=" O ILE C 35 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLY C 37 " --> pdb=" O LYS B 36 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA6, first strand: chain 'A' and resid 87 through 89 Processing sheet with id=AA7, first strand: chain 'A' and resid 95 through 97 Processing sheet with id=AA8, first strand: chain 'A' and resid 102 through 105 removed outlier: 6.605A pdb=" N SER A 102 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N SER B 105 " --> pdb=" O SER A 102 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE A 104 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N SER B 102 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N SER C 105 " --> pdb=" O SER B 102 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE B 104 " --> pdb=" O SER C 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 112 through 113 Processing sheet with id=AB1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AB2, first strand: chain 'A' and resid 145 through 152 removed outlier: 6.538A pdb=" N ALA A 145 " --> pdb=" O CYS B 146 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N VAL B 148 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLY A 147 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLY B 150 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N ILE A 149 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 9.227A pdb=" N ALA B 152 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N ILE A 151 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA B 145 " --> pdb=" O CYS C 146 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL C 148 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N GLY B 147 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N GLY C 150 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N ILE B 149 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 9.219A pdb=" N ALA C 152 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N ILE B 151 " --> pdb=" O ALA C 152 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 26 hydrogen bonds defined for protein. 78 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: 0.32 Time building geometry restraints manager: 0.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 886 1.33 - 1.45: 282 1.45 - 1.57: 1481 1.57 - 1.69: 0 1.69 - 1.81: 9 Bond restraints: 2658 Sorted by residual: bond pdb=" CB ASN A 19 " pdb=" CG ASN A 19 " ideal model delta sigma weight residual 1.516 1.475 0.041 2.50e-02 1.60e+03 2.74e+00 bond pdb=" CB ASN C 19 " pdb=" CG ASN C 19 " ideal model delta sigma weight residual 1.516 1.476 0.040 2.50e-02 1.60e+03 2.61e+00 bond pdb=" CB ASN B 19 " pdb=" CG ASN B 19 " ideal model delta sigma weight residual 1.516 1.476 0.040 2.50e-02 1.60e+03 2.60e+00 bond pdb=" CB VAL B 118 " pdb=" CG1 VAL B 118 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.35e+00 bond pdb=" CB VAL C 118 " pdb=" CG1 VAL C 118 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.32e+00 ... (remaining 2653 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 3446 2.41 - 4.82: 118 4.82 - 7.23: 12 7.23 - 9.64: 0 9.64 - 12.05: 3 Bond angle restraints: 3579 Sorted by residual: angle pdb=" CA LEU A 42 " pdb=" CB LEU A 42 " pdb=" CG LEU A 42 " ideal model delta sigma weight residual 116.30 128.35 -12.05 3.50e+00 8.16e-02 1.18e+01 angle pdb=" CA LEU B 42 " pdb=" CB LEU B 42 " pdb=" CG LEU B 42 " ideal model delta sigma weight residual 116.30 128.30 -12.00 3.50e+00 8.16e-02 1.18e+01 angle pdb=" CA LEU C 42 " pdb=" CB LEU C 42 " pdb=" CG LEU C 42 " ideal model delta sigma weight residual 116.30 128.30 -12.00 3.50e+00 8.16e-02 1.17e+01 angle pdb=" N ASP A 124 " pdb=" CA ASP A 124 " pdb=" C ASP A 124 " ideal model delta sigma weight residual 110.80 117.81 -7.01 2.13e+00 2.20e-01 1.08e+01 angle pdb=" N ASP C 124 " pdb=" CA ASP C 124 " pdb=" C ASP C 124 " ideal model delta sigma weight residual 110.80 117.78 -6.98 2.13e+00 2.20e-01 1.07e+01 ... (remaining 3574 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.91: 1326 15.91 - 31.83: 177 31.83 - 47.74: 39 47.74 - 63.66: 3 63.66 - 79.57: 9 Dihedral angle restraints: 1554 sinusoidal: 585 harmonic: 969 Sorted by residual: dihedral pdb=" CA ILE B 18 " pdb=" C ILE B 18 " pdb=" N ASN B 19 " pdb=" CA ASN B 19 " ideal model delta harmonic sigma weight residual 180.00 153.12 26.88 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA ILE C 18 " pdb=" C ILE C 18 " pdb=" N ASN C 19 " pdb=" CA ASN C 19 " ideal model delta harmonic sigma weight residual 180.00 153.17 26.83 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA ILE A 18 " pdb=" C ILE A 18 " pdb=" N ASN A 19 " pdb=" CA ASN A 19 " ideal model delta harmonic sigma weight residual 180.00 153.18 26.82 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 1551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 251 0.045 - 0.091: 110 0.091 - 0.136: 35 0.136 - 0.181: 12 0.181 - 0.226: 3 Chirality restraints: 411 Sorted by residual: chirality pdb=" CB VAL B 118 " pdb=" CA VAL B 118 " pdb=" CG1 VAL B 118 " pdb=" CG2 VAL B 118 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB VAL A 118 " pdb=" CA VAL A 118 " pdb=" CG1 VAL A 118 " pdb=" CG2 VAL A 118 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB VAL C 118 " pdb=" CA VAL C 118 " pdb=" CG1 VAL C 118 " pdb=" CG2 VAL C 118 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 408 not shown) Planarity restraints: 474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 20 " 0.018 2.00e-02 2.50e+03 1.35e-02 3.21e+00 pdb=" CG PHE B 20 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE B 20 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 20 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 20 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 20 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 20 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 20 " 0.018 2.00e-02 2.50e+03 1.35e-02 3.20e+00 pdb=" CG PHE A 20 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE A 20 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 20 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 20 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 20 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 20 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 20 " 0.018 2.00e-02 2.50e+03 1.35e-02 3.18e+00 pdb=" CG PHE C 20 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE C 20 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE C 20 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE C 20 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 20 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 20 " 0.002 2.00e-02 2.50e+03 ... (remaining 471 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 36 2.56 - 3.14: 2294 3.14 - 3.73: 3944 3.73 - 4.31: 5191 4.31 - 4.90: 9443 Nonbonded interactions: 20908 Sorted by model distance: nonbonded pdb=" ND2 ASN A 53 " pdb=" O VAL C 14 " model vdw 1.971 3.120 nonbonded pdb=" OG1 THR A 137 " pdb=" O THR B 137 " model vdw 2.129 3.040 nonbonded pdb=" OG1 THR B 137 " pdb=" O THR C 137 " model vdw 2.160 3.040 nonbonded pdb=" ND1 HIS A 46 " pdb=" OE1 GLU B 100 " model vdw 2.204 3.120 nonbonded pdb=" N SER A 142 " pdb=" OG SER B 142 " model vdw 2.208 3.120 ... (remaining 20903 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.390 Find NCS groups from input model: 0.020 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:6.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4319 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 : 0.009 0.051 2658 Z= 0.383 Angle : 1.063 12.048 3579 Z= 0.566 Chirality : 0.060 0.226 411 Planarity : 0.006 0.034 474 Dihedral : 16.233 79.572 942 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 38.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.50 % Favored : 73.50 % Rotamer: Outliers : 0.00 % Allowed : 19.50 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.56 (0.29), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.23 (0.22), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 115 PHE 0.030 0.004 PHE A 20 TRP 0.004 0.002 TRP A 32 HIS 0.009 0.003 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00936 ( 2658) covalent geometry : angle 1.06277 ( 3579) hydrogen bonds : bond 0.28830 ( 26) hydrogen bonds : angle 16.72516 ( 78) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.5871 (ttm170) cc_final: 0.5295 (tpm170) REVERT: A 143 ARG cc_start: 0.5537 (ptt180) cc_final: 0.4431 (mmp-170) REVERT: C 116 THR cc_start: 0.5679 (m) cc_final: 0.5469 (p) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.3578 time to fit residues: 40.9021 Evaluate side-chains 35 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS B 15 GLN B 48 HIS C 15 GLN C 48 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.211236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.195599 restraints weight = 5220.074| |-----------------------------------------------------------------------------| r_work (start): 0.4746 rms_B_bonded: 3.02 r_work: 0.4651 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5119 moved from start: 0.6145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2658 Z= 0.194 Angle : 0.856 8.750 3579 Z= 0.454 Chirality : 0.054 0.169 411 Planarity : 0.004 0.023 474 Dihedral : 7.045 23.475 363 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.38 % Favored : 84.62 % Rotamer: Outliers : 13.48 % Allowed : 26.60 % Favored : 59.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.95 (0.30), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.76 (0.23), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 143 PHE 0.020 0.004 PHE B 50 TRP 0.004 0.001 TRP C 32 HIS 0.006 0.001 HIS C 48 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 2658) covalent geometry : angle 0.85630 ( 3579) hydrogen bonds : bond 0.05778 ( 26) hydrogen bonds : angle 9.39224 ( 78) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 55 time to evaluate : 0.107 Fit side-chains REVERT: A 115 ARG cc_start: 0.6072 (ttm170) cc_final: 0.5714 (tpm170) REVERT: A 122 LYS cc_start: 0.4104 (OUTLIER) cc_final: 0.3788 (mttt) REVERT: A 143 ARG cc_start: 0.5454 (ptt180) cc_final: 0.3970 (mmp80) REVERT: B 46 HIS cc_start: 0.4665 (m90) cc_final: 0.4381 (p-80) REVERT: C 50 PHE cc_start: 0.6166 (OUTLIER) cc_final: 0.5939 (p90) outliers start: 38 outliers final: 10 residues processed: 87 average time/residue: 0.3346 time to fit residues: 30.0810 Evaluate side-chains 37 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 25 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 50 PHE Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 0.0770 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 35 optimal weight: 0.0370 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.6016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.208534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.192324 restraints weight = 5346.839| |-----------------------------------------------------------------------------| r_work (start): 0.4730 rms_B_bonded: 3.07 r_work: 0.4645 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5542 moved from start: 0.8231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2658 Z= 0.162 Angle : 0.761 7.218 3579 Z= 0.398 Chirality : 0.050 0.150 411 Planarity : 0.003 0.016 474 Dihedral : 5.736 21.482 363 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.95 % Favored : 84.05 % Rotamer: Outliers : 11.70 % Allowed : 30.85 % Favored : 57.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.62 (0.32), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 143 PHE 0.010 0.002 PHE B 20 TRP 0.005 0.001 TRP C 32 HIS 0.006 0.001 HIS B 48 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 2658) covalent geometry : angle 0.76058 ( 3579) hydrogen bonds : bond 0.05567 ( 26) hydrogen bonds : angle 8.12574 ( 78) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 33 time to evaluate : 0.073 Fit side-chains REVERT: A 122 LYS cc_start: 0.4812 (OUTLIER) cc_final: 0.4372 (mttt) REVERT: A 143 ARG cc_start: 0.5594 (ptt180) cc_final: 0.4050 (mmp80) REVERT: B 112 ILE cc_start: 0.8670 (mp) cc_final: 0.8469 (mt) REVERT: C 8 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6501 (tp) REVERT: C 9 LYS cc_start: 0.5148 (pptt) cc_final: 0.4783 (pptt) REVERT: C 50 PHE cc_start: 0.6167 (OUTLIER) cc_final: 0.5925 (p90) REVERT: C 52 ASP cc_start: 0.4853 (OUTLIER) cc_final: 0.4611 (t0) REVERT: C 117 LEU cc_start: 0.4641 (tp) cc_final: 0.3602 (pt) REVERT: C 122 LYS cc_start: 0.2139 (OUTLIER) cc_final: 0.1808 (mmpt) outliers start: 33 outliers final: 9 residues processed: 61 average time/residue: 0.3686 time to fit residues: 23.2348 Evaluate side-chains 39 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 25 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 50 PHE Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 122 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 18 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 HIS ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.202166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.184262 restraints weight = 5467.484| |-----------------------------------------------------------------------------| r_work (start): 0.4682 rms_B_bonded: 3.05 r_work: 0.4593 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6115 moved from start: 1.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2658 Z= 0.200 Angle : 0.856 9.012 3579 Z= 0.446 Chirality : 0.055 0.198 411 Planarity : 0.003 0.020 474 Dihedral : 6.921 27.975 363 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.80 % Favored : 81.20 % Rotamer: Outliers : 10.28 % Allowed : 34.04 % Favored : 55.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.53 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 143 PHE 0.031 0.005 PHE B 20 TRP 0.008 0.002 TRP A 32 HIS 0.005 0.001 HIS B 48 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 2658) covalent geometry : angle 0.85610 ( 3579) hydrogen bonds : bond 0.06247 ( 26) hydrogen bonds : angle 8.57285 ( 78) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 33 time to evaluate : 0.075 Fit side-chains REVERT: A 21 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6800 (pm20) REVERT: A 48 HIS cc_start: 0.5840 (OUTLIER) cc_final: 0.5620 (m90) REVERT: A 122 LYS cc_start: 0.5733 (OUTLIER) cc_final: 0.5259 (mttt) REVERT: A 143 ARG cc_start: 0.6306 (ptt180) cc_final: 0.4007 (mmp-170) REVERT: B 50 PHE cc_start: 0.5998 (OUTLIER) cc_final: 0.5658 (t80) REVERT: B 101 ASP cc_start: 0.5603 (OUTLIER) cc_final: 0.4945 (m-30) REVERT: C 8 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6972 (tm) REVERT: C 111 CYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8169 (m) outliers start: 29 outliers final: 11 residues processed: 56 average time/residue: 0.3468 time to fit residues: 20.0786 Evaluate side-chains 40 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 23 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 50 PHE Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 25 optimal weight: 0.0270 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 1 optimal weight: 0.4980 chunk 30 optimal weight: 0.0050 chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.2650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4955 r_free = 0.4955 target = 0.210126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.192587 restraints weight = 5206.961| |-----------------------------------------------------------------------------| r_work (start): 0.4764 rms_B_bonded: 3.08 r_work: 0.4674 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.4674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5921 moved from start: 1.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2658 Z= 0.129 Angle : 0.692 7.370 3579 Z= 0.355 Chirality : 0.049 0.151 411 Planarity : 0.002 0.012 474 Dihedral : 5.615 22.810 363 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.81 % Favored : 85.19 % Rotamer: Outliers : 9.22 % Allowed : 34.75 % Favored : 56.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.43 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 143 PHE 0.011 0.002 PHE B 20 TRP 0.006 0.001 TRP C 32 HIS 0.004 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 2658) covalent geometry : angle 0.69204 ( 3579) hydrogen bonds : bond 0.04217 ( 26) hydrogen bonds : angle 7.75673 ( 78) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 25 time to evaluate : 0.058 Fit side-chains REVERT: A 50 PHE cc_start: 0.5065 (OUTLIER) cc_final: 0.3575 (t80) REVERT: A 122 LYS cc_start: 0.5846 (OUTLIER) cc_final: 0.5529 (mttt) REVERT: B 50 PHE cc_start: 0.5804 (OUTLIER) cc_final: 0.5257 (t80) REVERT: C 18 ILE cc_start: 0.4891 (OUTLIER) cc_final: 0.4221 (mt) REVERT: C 88 THR cc_start: 0.6502 (OUTLIER) cc_final: 0.6090 (t) REVERT: C 111 CYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8171 (m) REVERT: C 126 LEU cc_start: 0.1163 (OUTLIER) cc_final: 0.0820 (tp) outliers start: 26 outliers final: 8 residues processed: 47 average time/residue: 0.3272 time to fit residues: 15.9459 Evaluate side-chains 37 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 22 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 PHE Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 126 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 35 optimal weight: 0.0570 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 0.0980 chunk 14 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 9 optimal weight: 0.0770 chunk 27 optimal weight: 1.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4986 r_free = 0.4986 target = 0.212940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.194940 restraints weight = 5238.723| |-----------------------------------------------------------------------------| r_work (start): 0.4777 rms_B_bonded: 3.03 r_work: 0.4693 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5927 moved from start: 1.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2658 Z= 0.128 Angle : 0.701 11.104 3579 Z= 0.350 Chirality : 0.049 0.146 411 Planarity : 0.002 0.013 474 Dihedral : 5.314 18.828 363 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.66 % Favored : 82.34 % Rotamer: Outliers : 9.57 % Allowed : 34.04 % Favored : 56.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.37 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 115 PHE 0.013 0.002 PHE B 20 TRP 0.004 0.001 TRP C 32 HIS 0.005 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 2658) covalent geometry : angle 0.70088 ( 3579) hydrogen bonds : bond 0.04175 ( 26) hydrogen bonds : angle 7.18014 ( 78) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 24 time to evaluate : 0.107 Fit side-chains REVERT: A 50 PHE cc_start: 0.4959 (OUTLIER) cc_final: 0.3704 (t80) REVERT: A 122 LYS cc_start: 0.6158 (OUTLIER) cc_final: 0.5803 (mttt) REVERT: B 50 PHE cc_start: 0.5772 (OUTLIER) cc_final: 0.5245 (t80) REVERT: C 9 LYS cc_start: 0.5717 (pptt) cc_final: 0.5428 (pptt) REVERT: C 18 ILE cc_start: 0.4737 (pp) cc_final: 0.4031 (mt) REVERT: C 88 THR cc_start: 0.6528 (OUTLIER) cc_final: 0.6112 (t) REVERT: C 111 CYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8147 (m) REVERT: C 117 LEU cc_start: 0.3709 (tp) cc_final: 0.3189 (pt) REVERT: C 126 LEU cc_start: 0.1072 (OUTLIER) cc_final: 0.0688 (tp) outliers start: 27 outliers final: 8 residues processed: 46 average time/residue: 0.3488 time to fit residues: 16.6608 Evaluate side-chains 34 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 20 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 PHE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 50 PHE Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 126 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 29 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 27 optimal weight: 0.0870 chunk 7 optimal weight: 0.0170 chunk 35 optimal weight: 0.0970 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5004 r_free = 0.5004 target = 0.214999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.197702 restraints weight = 5154.540| |-----------------------------------------------------------------------------| r_work (start): 0.4803 rms_B_bonded: 2.89 r_work: 0.4721 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5880 moved from start: 1.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2658 Z= 0.126 Angle : 0.711 9.739 3579 Z= 0.349 Chirality : 0.048 0.153 411 Planarity : 0.002 0.011 474 Dihedral : 5.099 18.477 363 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.96 % Favored : 86.04 % Rotamer: Outliers : 8.51 % Allowed : 32.62 % Favored : 58.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.31 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 143 PHE 0.012 0.002 PHE B 20 TRP 0.004 0.001 TRP C 32 HIS 0.004 0.001 HIS B 48 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 2658) covalent geometry : angle 0.71079 ( 3579) hydrogen bonds : bond 0.04316 ( 26) hydrogen bonds : angle 6.87183 ( 78) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 23 time to evaluate : 0.112 Fit side-chains REVERT: A 39 THR cc_start: 0.6532 (m) cc_final: 0.6308 (p) REVERT: A 50 PHE cc_start: 0.4737 (OUTLIER) cc_final: 0.3257 (t80) REVERT: A 122 LYS cc_start: 0.6304 (OUTLIER) cc_final: 0.5974 (mttt) REVERT: B 50 PHE cc_start: 0.5801 (OUTLIER) cc_final: 0.5287 (t80) REVERT: C 9 LYS cc_start: 0.5689 (pptt) cc_final: 0.5304 (pptt) REVERT: C 18 ILE cc_start: 0.4446 (pp) cc_final: 0.3836 (mt) REVERT: C 52 ASP cc_start: 0.5898 (p0) cc_final: 0.5027 (t0) REVERT: C 111 CYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8120 (m) REVERT: C 117 LEU cc_start: 0.3706 (tp) cc_final: 0.3175 (pt) REVERT: C 126 LEU cc_start: 0.1092 (OUTLIER) cc_final: 0.0716 (tp) outliers start: 24 outliers final: 9 residues processed: 45 average time/residue: 0.2938 time to fit residues: 13.7843 Evaluate side-chains 37 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 23 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 PHE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 50 PHE Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 126 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 12 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.201252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.182812 restraints weight = 5401.783| |-----------------------------------------------------------------------------| r_work (start): 0.4665 rms_B_bonded: 3.01 r_work: 0.4577 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6233 moved from start: 1.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 2658 Z= 0.211 Angle : 0.909 14.454 3579 Z= 0.447 Chirality : 0.052 0.176 411 Planarity : 0.003 0.018 474 Dihedral : 6.514 21.861 363 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.37 % Favored : 80.63 % Rotamer: Outliers : 8.87 % Allowed : 33.69 % Favored : 57.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.21 (0.34), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.26), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 143 PHE 0.031 0.005 PHE C 20 TRP 0.013 0.002 TRP A 32 HIS 0.011 0.002 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 2658) covalent geometry : angle 0.90936 ( 3579) hydrogen bonds : bond 0.06100 ( 26) hydrogen bonds : angle 7.76286 ( 78) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 26 time to evaluate : 0.099 Fit side-chains REVERT: A 50 PHE cc_start: 0.5834 (OUTLIER) cc_final: 0.4294 (t80) REVERT: A 122 LYS cc_start: 0.6305 (OUTLIER) cc_final: 0.5935 (ptpt) REVERT: A 143 ARG cc_start: 0.6429 (ptt180) cc_final: 0.4237 (mmp-170) REVERT: B 24 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.6371 (tp30) REVERT: B 50 PHE cc_start: 0.6202 (OUTLIER) cc_final: 0.5811 (t80) REVERT: C 9 LYS cc_start: 0.5595 (pptt) cc_final: 0.5188 (pptt) REVERT: C 18 ILE cc_start: 0.5546 (OUTLIER) cc_final: 0.4965 (mt) REVERT: C 126 LEU cc_start: 0.0827 (OUTLIER) cc_final: 0.0398 (tp) outliers start: 25 outliers final: 11 residues processed: 47 average time/residue: 0.3811 time to fit residues: 18.5363 Evaluate side-chains 33 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 16 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 50 PHE Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 50 PHE Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 126 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 12 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.204457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.185819 restraints weight = 5319.109| |-----------------------------------------------------------------------------| r_work (start): 0.4707 rms_B_bonded: 3.04 r_work: 0.4613 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 moved from start: 1.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2658 Z= 0.181 Angle : 0.847 9.071 3579 Z= 0.425 Chirality : 0.051 0.161 411 Planarity : 0.003 0.023 474 Dihedral : 6.335 21.652 363 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.95 % Favored : 84.05 % Rotamer: Outliers : 6.74 % Allowed : 35.82 % Favored : 57.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.25 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 115 PHE 0.024 0.003 PHE B 20 TRP 0.008 0.001 TRP A 32 HIS 0.005 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 2658) covalent geometry : angle 0.84664 ( 3579) hydrogen bonds : bond 0.05471 ( 26) hydrogen bonds : angle 7.70328 ( 78) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 21 time to evaluate : 0.099 Fit side-chains REVERT: A 50 PHE cc_start: 0.5714 (OUTLIER) cc_final: 0.4348 (t80) REVERT: A 122 LYS cc_start: 0.6530 (OUTLIER) cc_final: 0.6182 (ptpt) REVERT: B 24 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.6462 (tp30) REVERT: B 50 PHE cc_start: 0.6382 (OUTLIER) cc_final: 0.5993 (t80) REVERT: C 9 LYS cc_start: 0.5338 (pptt) cc_final: 0.5002 (pptt) REVERT: C 18 ILE cc_start: 0.5679 (OUTLIER) cc_final: 0.5091 (mt) outliers start: 19 outliers final: 10 residues processed: 38 average time/residue: 0.4164 time to fit residues: 16.2930 Evaluate side-chains 31 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 16 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 PHE Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 50 PHE Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 GLN C 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.201937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.184722 restraints weight = 5502.974| |-----------------------------------------------------------------------------| r_work (start): 0.4674 rms_B_bonded: 2.90 r_work: 0.4593 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6245 moved from start: 1.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2658 Z= 0.196 Angle : 0.885 9.869 3579 Z= 0.444 Chirality : 0.051 0.142 411 Planarity : 0.003 0.029 474 Dihedral : 6.561 21.419 363 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.80 % Favored : 81.20 % Rotamer: Outliers : 6.38 % Allowed : 38.30 % Favored : 55.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.26 (0.34), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.26), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 115 PHE 0.027 0.004 PHE C 20 TRP 0.007 0.002 TRP A 32 HIS 0.007 0.002 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 2658) covalent geometry : angle 0.88468 ( 3579) hydrogen bonds : bond 0.05566 ( 26) hydrogen bonds : angle 8.11979 ( 78) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 26 time to evaluate : 0.060 Fit side-chains REVERT: A 50 PHE cc_start: 0.6011 (OUTLIER) cc_final: 0.4660 (t80) REVERT: A 122 LYS cc_start: 0.6763 (OUTLIER) cc_final: 0.6302 (ptpt) REVERT: B 24 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6637 (tp30) REVERT: B 50 PHE cc_start: 0.6552 (OUTLIER) cc_final: 0.6173 (t80) REVERT: C 9 LYS cc_start: 0.5405 (pptt) cc_final: 0.5068 (pptt) REVERT: C 18 ILE cc_start: 0.5757 (OUTLIER) cc_final: 0.5199 (mt) REVERT: C 40 GLU cc_start: 0.6292 (OUTLIER) cc_final: 0.5647 (pp20) outliers start: 18 outliers final: 11 residues processed: 42 average time/residue: 0.4429 time to fit residues: 19.1543 Evaluate side-chains 39 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 22 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 PHE Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 50 PHE Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 22 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 33 optimal weight: 0.0970 chunk 23 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN C 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4936 r_free = 0.4936 target = 0.208289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.190893 restraints weight = 5238.963| |-----------------------------------------------------------------------------| r_work (start): 0.4739 rms_B_bonded: 2.92 r_work: 0.4652 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6127 moved from start: 1.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2658 Z= 0.152 Angle : 0.815 7.736 3579 Z= 0.413 Chirality : 0.049 0.144 411 Planarity : 0.003 0.025 474 Dihedral : 6.128 21.784 363 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.52 % Favored : 83.48 % Rotamer: Outliers : 7.09 % Allowed : 38.65 % Favored : 54.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.23 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 143 PHE 0.015 0.002 PHE B 20 TRP 0.005 0.001 TRP A 32 HIS 0.004 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 2658) covalent geometry : angle 0.81462 ( 3579) hydrogen bonds : bond 0.05099 ( 26) hydrogen bonds : angle 7.40941 ( 78) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1076.52 seconds wall clock time: 18 minutes 59.36 seconds (1139.36 seconds total)