Starting phenix.real_space_refine on Mon Feb 10 21:23:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vzf_32227/02_2025/7vzf_32227.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vzf_32227/02_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_32227/02_2025/7vzf_32227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vzf_32227/02_2025/7vzf_32227.map" model { file = "/net/cci-nas-00/data/ceres_data/7vzf_32227/02_2025/7vzf_32227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vzf_32227/02_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-5592/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: 2.40, per 1000 atoms: 0.91 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: 0.58 Conformation dependent library (CDL) restraints added in 313.6 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: 0.35 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: 0.57 Time building geometry restraints manager: 0.69 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: 1.500 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: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.530 Find NCS groups from input model: 0.040 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:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.470 ------------------------------------------------------------------------------- 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: 0.8097 time to fit residues: 92.6634 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 : 0.284 ------------------------------------------------------------------------------- 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 = 44)----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.193119 restraints weight = 5407.743| |-----------------------------------------------------------------------------| r_work (start): 0.4722 rms_B_bonded: 3.03 r_work: 0.4635 rms_B_bonded: 3.53 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 : 0.281 Fit side-chains REVERT: A 115 ARG cc_start: 0.6152 (ttm170) cc_final: 0.5816 (tpm170) REVERT: A 122 LYS cc_start: 0.4339 (OUTLIER) cc_final: 0.3958 (mttt) REVERT: A 143 ARG cc_start: 0.5515 (ptt180) cc_final: 0.3955 (mmp80) REVERT: B 46 HIS cc_start: 0.5048 (m90) cc_final: 0.4562 (p-80) outliers start: 38 outliers final: 10 residues processed: 82 average time/residue: 0.7599 time to fit residues: 64.5016 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 : 0.312 ------------------------------------------------------------------------------- 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: 10.0000 chunk 16 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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 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 = 0.4839 r_free = 0.4839 target = 0.197235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.179836 restraints weight = 5350.935| |-----------------------------------------------------------------------------| r_work (start): 0.4629 rms_B_bonded: 3.06 r_work: 0.4544 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6162 moved from start: 1.0548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 2658 Z= 0.365 Angle : 0.927 10.620 3579 Z= 0.488 Chirality : 0.056 0.183 411 Planarity : 0.004 0.021 474 Dihedral : 7.252 26.902 363 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.08 % Favored : 78.92 % Rotamer: Outliers : 12.06 % Allowed : 31.56 % 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 (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: -4.81 (0.32), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.66 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 32 HIS 0.007 0.002 HIS C 43 PHE 0.028 0.005 PHE C 20 ARG 0.003 0.001 ARG A 115 *********************** 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: 34 poor density : 37 time to evaluate : 0.297 Fit side-chains REVERT: A 21 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6809 (pm20) REVERT: A 50 PHE cc_start: 0.5570 (OUTLIER) cc_final: 0.4593 (t80) REVERT: A 115 ARG cc_start: 0.6834 (ttm170) cc_final: 0.6170 (tpm170) REVERT: A 122 LYS cc_start: 0.4998 (OUTLIER) cc_final: 0.4569 (mttt) REVERT: A 143 ARG cc_start: 0.6392 (ptt180) cc_final: 0.4060 (mmp-170) REVERT: B 50 PHE cc_start: 0.6193 (OUTLIER) cc_final: 0.5811 (t80) REVERT: B 133 GLU cc_start: 0.3690 (OUTLIER) cc_final: 0.3440 (tt0) REVERT: C 9 LYS cc_start: 0.5830 (pptt) cc_final: 0.5487 (pptt) outliers start: 34 outliers final: 11 residues processed: 65 average time/residue: 0.9149 time to fit residues: 61.3611 Evaluate side-chains 38 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 23 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 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 B residue 133 GLU 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: 0.9990 chunk 33 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 0.0670 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.204190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.186691 restraints weight = 5416.317| |-----------------------------------------------------------------------------| r_work (start): 0.4688 rms_B_bonded: 3.03 r_work: 0.4607 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6060 moved from start: 1.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2658 Z= 0.227 Angle : 0.756 7.781 3579 Z= 0.389 Chirality : 0.050 0.172 411 Planarity : 0.003 0.016 474 Dihedral : 6.332 25.280 363 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.95 % Favored : 84.05 % Rotamer: Outliers : 9.22 % Allowed : 35.11 % 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 (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: -4.55 (0.32), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 32 HIS 0.009 0.001 HIS A 43 PHE 0.015 0.002 PHE B 20 ARG 0.001 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 53 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 27 time to evaluate : 0.294 Fit side-chains REVERT: A 115 ARG cc_start: 0.6673 (ttm170) cc_final: 0.6171 (tpm170) REVERT: A 122 LYS cc_start: 0.5436 (OUTLIER) cc_final: 0.5028 (mttt) REVERT: A 143 ARG cc_start: 0.6162 (ptt180) cc_final: 0.3992 (mmp80) REVERT: B 24 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.6412 (tp30) REVERT: C 9 LYS cc_start: 0.5237 (pptt) cc_final: 0.4999 (pptt) REVERT: C 88 THR cc_start: 0.6535 (OUTLIER) cc_final: 0.6108 (t) outliers start: 26 outliers final: 13 residues processed: 49 average time/residue: 0.8222 time to fit residues: 41.7847 Evaluate side-chains 37 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 21 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 31 optimal weight: 1.9990 chunk 2 optimal weight: 0.0970 chunk 18 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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** ** B 43 HIS ** 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 = 0.4881 r_free = 0.4881 target = 0.201291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.183783 restraints weight = 5295.987| |-----------------------------------------------------------------------------| r_work (start): 0.4677 rms_B_bonded: 2.96 r_work: 0.4593 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6189 moved from start: 1.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2658 Z= 0.260 Angle : 0.808 8.855 3579 Z= 0.413 Chirality : 0.051 0.174 411 Planarity : 0.003 0.017 474 Dihedral : 6.332 22.247 363 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.94 % Favored : 80.06 % Rotamer: Outliers : 11.35 % Allowed : 34.75 % 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: -4.50 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 32 HIS 0.010 0.001 HIS A 43 PHE 0.022 0.003 PHE B 20 ARG 0.002 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 57 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 25 time to evaluate : 0.289 Fit side-chains REVERT: A 115 ARG cc_start: 0.6926 (ttm170) cc_final: 0.6433 (tpm170) REVERT: A 122 LYS cc_start: 0.6150 (OUTLIER) cc_final: 0.5811 (ptpt) REVERT: B 50 PHE cc_start: 0.6254 (OUTLIER) cc_final: 0.5887 (t80) REVERT: C 9 LYS cc_start: 0.5603 (pptt) cc_final: 0.5283 (pptt) REVERT: C 18 ILE cc_start: 0.5036 (OUTLIER) cc_final: 0.4403 (mt) REVERT: C 52 ASP cc_start: 0.6309 (p0) cc_final: 0.5356 (OUTLIER) outliers start: 32 outliers final: 14 residues processed: 52 average time/residue: 0.8102 time to fit residues: 43.8054 Evaluate side-chains 37 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 21 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 88 THR 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 50 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 88 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 116 THR 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: 4.9990 chunk 22 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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** ** B 43 HIS ** 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 = 0.4859 r_free = 0.4859 target = 0.199740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.181617 restraints weight = 5401.619| |-----------------------------------------------------------------------------| r_work (start): 0.4655 rms_B_bonded: 3.09 r_work: 0.4571 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6262 moved from start: 1.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2658 Z= 0.308 Angle : 0.874 9.665 3579 Z= 0.445 Chirality : 0.052 0.166 411 Planarity : 0.003 0.021 474 Dihedral : 6.601 21.545 363 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.09 % Favored : 80.91 % Rotamer: Outliers : 12.41 % Allowed : 34.40 % Favored : 53.19 % 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: -4.48 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 32 HIS 0.010 0.001 HIS A 43 PHE 0.023 0.004 PHE B 20 ARG 0.003 0.001 ARG A 115 *********************** 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 58 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 23 time to evaluate : 0.302 Fit side-chains REVERT: A 50 PHE cc_start: 0.5971 (OUTLIER) cc_final: 0.4545 (t80) REVERT: A 115 ARG cc_start: 0.7109 (ttm170) cc_final: 0.6365 (tpm170) REVERT: A 122 LYS cc_start: 0.6164 (OUTLIER) cc_final: 0.5804 (ptpt) REVERT: B 24 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.6297 (tp30) REVERT: B 50 PHE cc_start: 0.6278 (OUTLIER) cc_final: 0.5768 (t80) REVERT: C 9 LYS cc_start: 0.5548 (pptt) cc_final: 0.5189 (pptt) REVERT: C 18 ILE cc_start: 0.5289 (OUTLIER) cc_final: 0.4554 (mm) REVERT: C 40 GLU cc_start: 0.6353 (OUTLIER) cc_final: 0.5037 (pm20) REVERT: C 120 HIS cc_start: 0.7382 (OUTLIER) cc_final: 0.6589 (m90) outliers start: 35 outliers final: 15 residues processed: 54 average time/residue: 0.7497 time to fit residues: 42.0671 Evaluate side-chains 42 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 20 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 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 87 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 38 LEU 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 116 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 120 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 31 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 35 optimal weight: 0.1980 chunk 21 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** B 43 HIS C 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4914 r_free = 0.4914 target = 0.204995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.186361 restraints weight = 5390.166| |-----------------------------------------------------------------------------| r_work (start): 0.4710 rms_B_bonded: 3.04 r_work: 0.4619 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6188 moved from start: 1.2493 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= 0.217 Angle : 0.790 9.592 3579 Z= 0.399 Chirality : 0.049 0.147 411 Planarity : 0.003 0.021 474 Dihedral : 6.039 20.913 363 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.95 % Favored : 82.05 % Rotamer: Outliers : 8.51 % Allowed : 36.88 % Favored : 54.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.40 (0.33), 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 0.005 0.001 TRP A 32 HIS 0.007 0.001 HIS A 43 PHE 0.015 0.002 PHE B 20 ARG 0.001 0.000 ARG C 143 *********************** 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 53 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 29 time to evaluate : 0.315 Fit side-chains REVERT: A 50 PHE cc_start: 0.5703 (OUTLIER) cc_final: 0.4325 (t80) REVERT: A 115 ARG cc_start: 0.7138 (ttm170) cc_final: 0.6560 (tpp-160) REVERT: A 122 LYS cc_start: 0.6293 (OUTLIER) cc_final: 0.5924 (ptpt) REVERT: B 24 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.6275 (tp30) REVERT: C 9 LYS cc_start: 0.5634 (pptt) cc_final: 0.5269 (pptt) REVERT: C 18 ILE cc_start: 0.5197 (OUTLIER) cc_final: 0.4501 (mm) REVERT: C 40 GLU cc_start: 0.6157 (OUTLIER) cc_final: 0.5025 (pm20) REVERT: C 120 HIS cc_start: 0.7491 (OUTLIER) cc_final: 0.6807 (m90) outliers start: 24 outliers final: 13 residues processed: 49 average time/residue: 0.8390 time to fit residues: 42.5933 Evaluate side-chains 42 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 23 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU 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 88 THR Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 38 LEU 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 116 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 120 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 0.0270 chunk 27 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.9442 ------------------------------------------------------------------------------- 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 = 0.4897 r_free = 0.4897 target = 0.203933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.186566 restraints weight = 5502.721| |-----------------------------------------------------------------------------| r_work (start): 0.4691 rms_B_bonded: 2.89 r_work: 0.4614 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6186 moved from start: 1.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2658 Z= 0.234 Angle : 0.806 8.652 3579 Z= 0.410 Chirality : 0.049 0.153 411 Planarity : 0.003 0.022 474 Dihedral : 6.024 20.483 363 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.23 % Favored : 81.77 % Rotamer: Outliers : 7.80 % Allowed : 38.30 % 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: -4.33 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 32 HIS 0.010 0.001 HIS B 43 PHE 0.018 0.002 PHE B 20 ARG 0.002 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 48 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 26 time to evaluate : 0.242 Fit side-chains REVERT: A 39 THR cc_start: 0.6542 (m) cc_final: 0.6311 (p) REVERT: A 50 PHE cc_start: 0.5666 (OUTLIER) cc_final: 0.4373 (t80) REVERT: A 115 ARG cc_start: 0.7204 (ttm170) cc_final: 0.6606 (tpp-160) REVERT: A 122 LYS cc_start: 0.6460 (OUTLIER) cc_final: 0.6068 (ptpt) REVERT: B 24 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.6328 (tp30) REVERT: B 50 PHE cc_start: 0.6392 (OUTLIER) cc_final: 0.5872 (t80) REVERT: C 9 LYS cc_start: 0.5474 (pptt) cc_final: 0.5064 (pptt) REVERT: C 18 ILE cc_start: 0.5411 (OUTLIER) cc_final: 0.4619 (mm) REVERT: C 40 GLU cc_start: 0.6231 (OUTLIER) cc_final: 0.5112 (pm20) REVERT: C 120 HIS cc_start: 0.7444 (OUTLIER) cc_final: 0.6769 (m90) REVERT: C 126 LEU cc_start: 0.0645 (OUTLIER) cc_final: 0.0242 (tp) outliers start: 22 outliers final: 11 residues processed: 45 average time/residue: 0.7416 time to fit residues: 34.7427 Evaluate side-chains 42 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 23 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU 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 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 116 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 120 HIS 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 13 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 = 0.4853 r_free = 0.4853 target = 0.198976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.181224 restraints weight = 5390.404| |-----------------------------------------------------------------------------| r_work (start): 0.4646 rms_B_bonded: 2.91 r_work: 0.4559 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 1.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 2658 Z= 0.335 Angle : 0.908 10.830 3579 Z= 0.461 Chirality : 0.053 0.167 411 Planarity : 0.003 0.026 474 Dihedral : 6.694 21.499 363 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.94 % Favored : 80.06 % Rotamer: Outliers : 9.57 % Allowed : 35.11 % 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 (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: -4.37 (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 TRP 0.007 0.002 TRP B 32 HIS 0.012 0.002 HIS A 43 PHE 0.026 0.004 PHE C 20 ARG 0.004 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 59 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 32 time to evaluate : 0.324 Fit side-chains REVERT: A 39 THR cc_start: 0.6555 (m) cc_final: 0.6349 (p) REVERT: A 50 PHE cc_start: 0.6054 (OUTLIER) cc_final: 0.4667 (t80) REVERT: A 115 ARG cc_start: 0.7451 (ttm170) cc_final: 0.6702 (tpp-160) REVERT: A 122 LYS cc_start: 0.6786 (OUTLIER) cc_final: 0.6322 (ptpt) REVERT: B 24 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.6455 (tp30) REVERT: B 50 PHE cc_start: 0.6525 (OUTLIER) cc_final: 0.6026 (t80) REVERT: C 18 ILE cc_start: 0.5494 (OUTLIER) cc_final: 0.4766 (mm) REVERT: C 40 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.5325 (pm20) REVERT: C 120 HIS cc_start: 0.7335 (OUTLIER) cc_final: 0.6620 (m90) outliers start: 27 outliers final: 13 residues processed: 54 average time/residue: 0.7670 time to fit residues: 43.0095 Evaluate side-chains 48 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 28 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 24 GLU 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 C residue 14 VAL 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 116 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 120 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 6 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 11 optimal weight: 0.0370 chunk 10 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 = 0.4900 r_free = 0.4900 target = 0.205090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.187094 restraints weight = 5253.022| |-----------------------------------------------------------------------------| r_work (start): 0.4692 rms_B_bonded: 2.97 r_work: 0.4602 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6164 moved from start: 1.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 2658 Z= 0.226 Angle : 0.798 7.989 3579 Z= 0.410 Chirality : 0.048 0.139 411 Planarity : 0.003 0.024 474 Dihedral : 6.047 22.291 363 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.38 % Favored : 82.62 % Rotamer: Outliers : 6.38 % Allowed : 40.43 % Favored : 53.19 % 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: -4.29 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 32 HIS 0.008 0.001 HIS B 43 PHE 0.014 0.002 PHE B 20 ARG 0.001 0.000 ARG A 115 ********************** 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 45 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 27 time to evaluate : 0.313 Fit side-chains REVERT: A 50 PHE cc_start: 0.5522 (OUTLIER) cc_final: 0.4302 (t80) REVERT: A 115 ARG cc_start: 0.7161 (ttm170) cc_final: 0.6650 (tpp-160) REVERT: A 122 LYS cc_start: 0.6715 (OUTLIER) cc_final: 0.6233 (ptpt) REVERT: B 50 PHE cc_start: 0.6407 (OUTLIER) cc_final: 0.5909 (t80) REVERT: C 18 ILE cc_start: 0.5478 (OUTLIER) cc_final: 0.4591 (mm) REVERT: C 40 GLU cc_start: 0.6317 (OUTLIER) cc_final: 0.5209 (pm20) REVERT: C 120 HIS cc_start: 0.7470 (OUTLIER) cc_final: 0.6855 (m90) REVERT: C 136 LYS cc_start: 0.7219 (pttp) cc_final: 0.6893 (tptt) outliers start: 18 outliers final: 8 residues processed: 44 average time/residue: 1.1038 time to fit residues: 49.9747 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 : 0.273 ------------------------------------------------------------------------------- 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 119 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 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 116 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 120 HIS 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 14 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 0.0030 chunk 22 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.1392 ------------------------------------------------------------------------------- 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 = 0.4873 r_free = 0.4873 target = 0.202397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.184547 restraints weight = 5294.876| |-----------------------------------------------------------------------------| r_work (start): 0.4669 rms_B_bonded: 2.94 r_work: 0.4580 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6252 moved from start: 1.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 2658 Z= 0.281 Angle : 0.848 8.779 3579 Z= 0.433 Chirality : 0.050 0.154 411 Planarity : 0.003 0.019 474 Dihedral : 6.125 21.067 363 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.80 % Favored : 81.20 % Rotamer: Outliers : 6.74 % Allowed : 40.43 % 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: -4.25 (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 TRP 0.005 0.001 TRP B 32 HIS 0.009 0.001 HIS A 43 PHE 0.020 0.003 PHE B 20 ARG 0.003 0.001 ARG A 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2216.92 seconds wall clock time: 39 minutes 52.53 seconds (2392.53 seconds total)