Starting phenix.real_space_refine on Wed Mar 5 16:18:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vzf_32227/03_2025/7vzf_32227.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vzf_32227/03_2025/7vzf_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_2025/7vzf_32227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vzf_32227/03_2025/7vzf_32227.map" model { file = "/net/cci-nas-00/data/ceres_data/7vzf_32227/03_2025/7vzf_32227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vzf_32227/03_2025/7vzf_32227.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: C, B Time building chain proxies: 2.10, per 1000 atoms: 0.80 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: 0.62 Conformation dependent library (CDL) restraints added in 336.0 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: 0.36 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: 0.54 Time building geometry restraints manager: 0.73 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 1.350 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.030 Find NCS groups from input model: 0.060 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:10.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.790 ------------------------------------------------------------------------------- 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= 0.654 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 : 38.45 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 (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: -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 TRP 0.004 0.002 TRP A 32 HIS 0.009 0.003 HIS B 43 PHE 0.030 0.004 PHE A 20 ARG 0.002 0.000 ARG B 115 *********************** 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 : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.5870 (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: 0.7743 time to fit residues: 88.6586 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 : 0.292 ------------------------------------------------------------------------------- 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: 0.8980 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 48 HIS B 15 GLN ** B 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4891 r_free = 0.4891 target = 0.208435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.193105 restraints weight = 5407.743| |-----------------------------------------------------------------------------| r_work (start): 0.4722 rms_B_bonded: 3.03 r_work: 0.4635 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5312 moved from start: 0.6593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 2658 Z= 0.311 Angle : 0.871 8.639 3579 Z= 0.463 Chirality : 0.054 0.142 411 Planarity : 0.004 0.022 474 Dihedral : 7.191 23.601 363 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.81 % Favored : 83.19 % Rotamer: Outliers : 13.48 % Allowed : 25.53 % Favored : 60.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.97 (0.31), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.78 (0.23), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 32 HIS 0.006 0.002 HIS C 48 PHE 0.026 0.005 PHE B 50 ARG 0.006 0.002 ARG B 143 *********************** 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 85 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 47 time to evaluate : 0.275 Fit side-chains REVERT: A 115 ARG cc_start: 0.6153 (ttm170) cc_final: 0.5817 (tpm170) REVERT: A 122 LYS cc_start: 0.4339 (OUTLIER) cc_final: 0.3958 (mttt) REVERT: A 143 ARG cc_start: 0.5516 (ptt180) cc_final: 0.3955 (mmp80) REVERT: B 46 HIS cc_start: 0.5049 (m90) cc_final: 0.4562 (p-80) outliers start: 38 outliers final: 10 residues processed: 82 average time/residue: 0.7318 time to fit residues: 62.1065 Evaluate side-chains 32 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 21 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 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 20 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 11 optimal weight: 0.4980 chunk 22 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 16 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 43 HIS A 48 HIS ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 HIS ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.198081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.180935 restraints weight = 5331.035| |-----------------------------------------------------------------------------| r_work (start): 0.4638 rms_B_bonded: 2.97 r_work: 0.4557 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6132 moved from start: 1.0544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 2658 Z= 0.353 Angle : 0.914 10.399 3579 Z= 0.479 Chirality : 0.055 0.180 411 Planarity : 0.004 0.020 474 Dihedral : 7.106 26.432 363 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.23 % Favored : 79.77 % Rotamer: Outliers : 11.35 % Allowed : 31.91 % Favored : 56.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.77 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.63 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 32 HIS 0.006 0.002 HIS C 43 PHE 0.028 0.005 PHE C 20 ARG 0.003 0.001 ARG C 143 *********************** 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 71 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 39 time to evaluate : 0.299 Fit side-chains REVERT: A 21 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6741 (pm20) REVERT: A 50 PHE cc_start: 0.5492 (OUTLIER) cc_final: 0.4541 (t80) REVERT: A 115 ARG cc_start: 0.6799 (ttm170) cc_final: 0.6177 (tpm170) REVERT: A 122 LYS cc_start: 0.4942 (OUTLIER) cc_final: 0.4417 (mttt) REVERT: A 143 ARG cc_start: 0.6356 (ptt180) cc_final: 0.4103 (mmp-170) REVERT: B 50 PHE cc_start: 0.6209 (OUTLIER) cc_final: 0.5804 (t80) REVERT: C 9 LYS cc_start: 0.5823 (pptt) cc_final: 0.5595 (pptt) outliers start: 32 outliers final: 13 residues processed: 65 average time/residue: 0.8662 time to fit residues: 58.1376 Evaluate side-chains 40 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 24 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 50 PHE Chi-restraints excluded: chain A residue 88 THR 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 103 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 21 optimal weight: 20.0000 chunk 32 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 1 optimal weight: 0.0170 chunk 14 optimal weight: 0.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4874 r_free = 0.4874 target = 0.201913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.183940 restraints weight = 5404.352| |-----------------------------------------------------------------------------| r_work (start): 0.4667 rms_B_bonded: 3.06 r_work: 0.4587 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6144 moved from start: 1.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 2658 Z= 0.270 Angle : 0.806 8.123 3579 Z= 0.411 Chirality : 0.051 0.177 411 Planarity : 0.003 0.017 474 Dihedral : 6.550 25.699 363 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.95 % Favored : 82.05 % Rotamer: Outliers : 10.64 % Allowed : 35.46 % Favored : 53.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.53 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 32 HIS 0.010 0.001 HIS A 43 PHE 0.019 0.003 PHE B 20 ARG 0.002 0.000 ARG A 115 *********************** 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 56 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 26 time to evaluate : 0.337 Fit side-chains REVERT: A 24 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7099 (tt0) REVERT: A 115 ARG cc_start: 0.6739 (ttm170) cc_final: 0.6258 (tpm170) REVERT: A 122 LYS cc_start: 0.5536 (OUTLIER) cc_final: 0.5198 (mttt) REVERT: A 133 GLU cc_start: 0.3644 (OUTLIER) cc_final: 0.3102 (tt0) REVERT: A 143 ARG cc_start: 0.6350 (ptt180) cc_final: 0.4098 (mmp-170) REVERT: B 24 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.6383 (tp30) REVERT: C 52 ASP cc_start: 0.4928 (OUTLIER) cc_final: 0.4683 (p0) outliers start: 30 outliers final: 16 residues processed: 53 average time/residue: 0.7459 time to fit residues: 41.2136 Evaluate side-chains 40 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 19 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU 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 103 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 24 GLU 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 14 VAL Chi-restraints excluded: chain C residue 50 PHE Chi-restraints excluded: chain C residue 52 ASP 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 116 THR 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 31 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 overall best weight: 2.3184 ------------------------------------------------------------------------------- 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 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.194422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.176177 restraints weight = 5314.860| |-----------------------------------------------------------------------------| r_work (start): 0.4598 rms_B_bonded: 3.07 r_work: 0.4514 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6381 moved from start: 1.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 2658 Z= 0.415 Angle : 0.978 14.177 3579 Z= 0.496 Chirality : 0.055 0.158 411 Planarity : 0.004 0.023 474 Dihedral : 7.372 28.887 363 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.51 % Favored : 79.49 % Rotamer: Outliers : 12.77 % Allowed : 34.75 % Favored : 52.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.56 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 32 HIS 0.012 0.002 HIS A 43 PHE 0.029 0.005 PHE B 20 ARG 0.004 0.001 ARG A 115 *********************** 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 64 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 28 time to evaluate : 0.291 Fit side-chains REVERT: A 50 PHE cc_start: 0.6204 (OUTLIER) cc_final: 0.4785 (t80) REVERT: A 115 ARG cc_start: 0.7315 (ttm170) cc_final: 0.6472 (tpm170) REVERT: A 122 LYS cc_start: 0.6185 (OUTLIER) cc_final: 0.5784 (ptpt) REVERT: A 133 GLU cc_start: 0.4408 (OUTLIER) cc_final: 0.3262 (tt0) REVERT: A 144 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7144 (pt) REVERT: B 24 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.6282 (tp30) REVERT: B 50 PHE cc_start: 0.6369 (OUTLIER) cc_final: 0.6008 (t80) REVERT: C 9 LYS cc_start: 0.5730 (pptt) cc_final: 0.5405 (pptt) REVERT: C 121 GLU cc_start: 0.6685 (mt-10) cc_final: 0.6455 (pm20) outliers start: 36 outliers final: 16 residues processed: 56 average time/residue: 0.8732 time to fit residues: 50.7100 Evaluate side-chains 45 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 23 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 HIS 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 112 ILE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 24 GLU 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 148 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 50 PHE Chi-restraints excluded: chain C residue 52 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 12 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 0.1980 chunk 23 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.4880 r_free = 0.4880 target = 0.201220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.183297 restraints weight = 5251.693| |-----------------------------------------------------------------------------| r_work (start): 0.4677 rms_B_bonded: 2.99 r_work: 0.4599 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6196 moved from start: 1.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2658 Z= 0.221 Angle : 0.806 10.943 3579 Z= 0.404 Chirality : 0.051 0.152 411 Planarity : 0.003 0.021 474 Dihedral : 6.420 24.823 363 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.23 % Favored : 81.77 % Rotamer: Outliers : 9.22 % Allowed : 37.94 % Favored : 52.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.41 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 32 HIS 0.007 0.001 HIS A 43 PHE 0.017 0.002 PHE B 20 ARG 0.001 0.000 ARG C 143 *********************** 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 57 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 31 time to evaluate : 0.311 Fit side-chains REVERT: A 115 ARG cc_start: 0.7111 (ttm170) cc_final: 0.6523 (tpp-160) REVERT: A 122 LYS cc_start: 0.6075 (OUTLIER) cc_final: 0.5761 (ptpt) REVERT: A 133 GLU cc_start: 0.3957 (OUTLIER) cc_final: 0.2960 (tt0) REVERT: B 50 PHE cc_start: 0.6231 (OUTLIER) cc_final: 0.5793 (t80) REVERT: C 9 LYS cc_start: 0.5808 (pptt) cc_final: 0.5420 (pptt) REVERT: C 52 ASP cc_start: 0.4725 (OUTLIER) cc_final: 0.4453 (m-30) outliers start: 26 outliers final: 11 residues processed: 52 average time/residue: 0.7985 time to fit residues: 43.0848 Evaluate side-chains 41 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 26 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 133 GLU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 50 PHE Chi-restraints excluded: chain C residue 52 ASP 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 116 THR Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 31 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 21 optimal weight: 30.0000 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 46 HIS ** 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 = 0.4887 r_free = 0.4887 target = 0.202252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.183170 restraints weight = 5283.388| |-----------------------------------------------------------------------------| r_work (start): 0.4675 rms_B_bonded: 3.13 r_work: 0.4587 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6215 moved from start: 1.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 2658 Z= 0.236 Angle : 0.814 9.615 3579 Z= 0.412 Chirality : 0.050 0.168 411 Planarity : 0.003 0.021 474 Dihedral : 6.096 22.344 363 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.80 % Favored : 81.20 % Rotamer: Outliers : 8.51 % Allowed : 37.94 % Favored : 53.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.36 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 32 HIS 0.009 0.001 HIS A 43 PHE 0.017 0.003 PHE B 20 ARG 0.002 0.000 ARG A 115 *********************** 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 51 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 27 time to evaluate : 0.300 Fit side-chains REVERT: A 115 ARG cc_start: 0.7253 (ttm170) cc_final: 0.6655 (tpp-160) REVERT: A 122 LYS cc_start: 0.6420 (OUTLIER) cc_final: 0.6060 (ptpt) REVERT: A 133 GLU cc_start: 0.3844 (OUTLIER) cc_final: 0.2833 (tt0) REVERT: B 24 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.6410 (tp30) REVERT: B 50 PHE cc_start: 0.6187 (OUTLIER) cc_final: 0.5727 (t80) REVERT: C 9 LYS cc_start: 0.5751 (pptt) cc_final: 0.5358 (pptt) outliers start: 24 outliers final: 12 residues processed: 47 average time/residue: 0.7474 time to fit residues: 36.5467 Evaluate side-chains 39 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 23 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 133 GLU 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 C residue 14 VAL Chi-restraints excluded: chain C residue 38 LEU 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 116 THR Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 28 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 0.0070 chunk 34 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 46 HIS ** 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 = 0.4875 r_free = 0.4875 target = 0.202301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.185073 restraints weight = 5384.853| |-----------------------------------------------------------------------------| r_work (start): 0.4667 rms_B_bonded: 2.95 r_work: 0.4588 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6162 moved from start: 1.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 2658 Z= 0.228 Angle : 0.798 9.041 3579 Z= 0.405 Chirality : 0.050 0.164 411 Planarity : 0.003 0.021 474 Dihedral : 5.964 21.627 363 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.09 % Favored : 82.91 % Rotamer: Outliers : 7.80 % Allowed : 39.72 % Favored : 52.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.28 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 32 HIS 0.007 0.001 HIS A 43 PHE 0.016 0.002 PHE B 20 ARG 0.001 0.000 ARG A 115 *********************** 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 49 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 27 time to evaluate : 0.328 Fit side-chains REVERT: A 115 ARG cc_start: 0.7217 (ttm170) cc_final: 0.6648 (tpp-160) REVERT: A 122 LYS cc_start: 0.6562 (OUTLIER) cc_final: 0.6248 (ptpt) REVERT: A 133 GLU cc_start: 0.3916 (OUTLIER) cc_final: 0.2893 (tt0) REVERT: A 144 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.6932 (pt) REVERT: B 24 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6504 (tp30) REVERT: B 50 PHE cc_start: 0.6220 (OUTLIER) cc_final: 0.5765 (t80) REVERT: C 9 LYS cc_start: 0.5496 (pptt) cc_final: 0.5088 (pptt) REVERT: C 52 ASP cc_start: 0.6157 (p0) cc_final: 0.5125 (OUTLIER) outliers start: 22 outliers final: 13 residues processed: 46 average time/residue: 0.8720 time to fit residues: 41.4989 Evaluate side-chains 41 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 24 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 144 LEU 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 C residue 14 VAL Chi-restraints excluded: chain C residue 38 LEU 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 116 THR Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 13 optimal weight: 0.0470 chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 4 optimal weight: 0.0670 chunk 25 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.2820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 HIS C 22 GLN ** C 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.198836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.181821 restraints weight = 5424.456| |-----------------------------------------------------------------------------| r_work (start): 0.4636 rms_B_bonded: 2.88 r_work: 0.4557 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6268 moved from start: 1.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 2658 Z= 0.286 Angle : 0.851 9.234 3579 Z= 0.433 Chirality : 0.051 0.173 411 Planarity : 0.003 0.023 474 Dihedral : 6.247 22.644 363 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.52 % Favored : 81.48 % Rotamer: Outliers : 8.51 % Allowed : 39.36 % Favored : 52.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.28 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.26), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 32 HIS 0.009 0.001 HIS A 43 PHE 0.024 0.003 PHE B 20 ARG 0.002 0.001 ARG A 115 *********************** 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 51 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 27 time to evaluate : 0.275 Fit side-chains REVERT: A 115 ARG cc_start: 0.7316 (ttm170) cc_final: 0.6722 (tpp-160) REVERT: A 122 LYS cc_start: 0.6816 (OUTLIER) cc_final: 0.6480 (ptpt) REVERT: A 144 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7195 (pt) REVERT: B 24 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.6700 (tp30) REVERT: B 50 PHE cc_start: 0.6121 (OUTLIER) cc_final: 0.5723 (t80) REVERT: C 9 LYS cc_start: 0.5584 (pptt) cc_final: 0.5369 (pptt) outliers start: 24 outliers final: 14 residues processed: 48 average time/residue: 1.0796 time to fit residues: 53.3015 Evaluate side-chains 42 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 24 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 144 LEU 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 C residue 14 VAL Chi-restraints excluded: chain C residue 38 LEU 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 116 THR 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 6 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 32 optimal weight: 0.0040 chunk 26 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 12 optimal weight: 0.0980 overall best weight: 0.5192 ------------------------------------------------------------------------------- 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** C 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.204093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.186719 restraints weight = 5353.415| |-----------------------------------------------------------------------------| r_work (start): 0.4684 rms_B_bonded: 2.97 r_work: 0.4596 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6148 moved from start: 1.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 2658 Z= 0.228 Angle : 0.799 8.239 3579 Z= 0.405 Chirality : 0.049 0.160 411 Planarity : 0.003 0.018 474 Dihedral : 5.809 20.840 363 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.52 % Favored : 83.48 % Rotamer: Outliers : 5.32 % Allowed : 43.26 % Favored : 51.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.18 (0.34), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.26), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 32 HIS 0.006 0.001 HIS A 43 PHE 0.014 0.002 PHE B 20 ARG 0.001 0.000 ARG C 143 ********************** 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 40 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 25 time to evaluate : 0.272 Fit side-chains REVERT: A 46 HIS cc_start: 0.5195 (m90) cc_final: 0.4798 (p-80) REVERT: A 115 ARG cc_start: 0.7196 (ttm170) cc_final: 0.6681 (tpp-160) REVERT: A 122 LYS cc_start: 0.6840 (OUTLIER) cc_final: 0.6520 (ptpt) REVERT: C 9 LYS cc_start: 0.5500 (pptt) cc_final: 0.5114 (pptt) REVERT: C 136 LYS cc_start: 0.7046 (pttp) cc_final: 0.6811 (tptt) outliers start: 15 outliers final: 10 residues processed: 39 average time/residue: 0.8780 time to fit residues: 35.5015 Evaluate side-chains 34 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 23 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain C residue 38 LEU 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 116 THR 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: 0.7980 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 46 HIS ** 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 = 0.4880 r_free = 0.4880 target = 0.202548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.185395 restraints weight = 5374.822| |-----------------------------------------------------------------------------| r_work (start): 0.4676 rms_B_bonded: 2.93 r_work: 0.4599 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6194 moved from start: 1.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 2658 Z= 0.254 Angle : 0.810 7.960 3579 Z= 0.410 Chirality : 0.050 0.167 411 Planarity : 0.003 0.015 474 Dihedral : 5.850 20.905 363 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.23 % Favored : 81.77 % Rotamer: Outliers : 6.74 % Allowed : 42.20 % Favored : 51.06 % 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: -4.18 (0.34), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.26), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 32 HIS 0.008 0.001 HIS A 43 PHE 0.020 0.003 PHE B 20 ARG 0.002 0.000 ARG A 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2219.50 seconds wall clock time: 38 minutes 44.89 seconds (2324.89 seconds total)