Starting phenix.real_space_refine on Wed Mar 4 07:30:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wkw_32570/03_2026/7wkw_32570_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wkw_32570/03_2026/7wkw_32570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wkw_32570/03_2026/7wkw_32570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wkw_32570/03_2026/7wkw_32570.map" model { file = "/net/cci-nas-00/data/ceres_data/7wkw_32570/03_2026/7wkw_32570_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wkw_32570/03_2026/7wkw_32570_trim.cif" } resolution = 2.62 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians S 42 5.16 5 C 3938 2.51 5 N 940 2.21 5 O 998 1.98 5 H 6138 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12056 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 6006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 6006 Classifications: {'peptide': 377} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 359} Chain breaks: 1 Chain: "A" Number of atoms: 6006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 6006 Classifications: {'peptide': 377} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 359} Chain breaks: 1 Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'E7O': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'E7O': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.74, per 1000 atoms: 0.23 Number of scatterers: 12056 At special positions: 0 Unit cell: (80.845, 121.693, 71.484, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 O 998 8.00 N 940 7.00 C 3938 6.00 H 6138 1.00 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: 0.93 Conformation dependent library (CDL) restraints added in 424.5 milliseconds 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1420 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 2 sheets defined 80.1% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'B' and resid 3 through 30 removed outlier: 3.886A pdb=" N LEU B 7 " --> pdb=" O SER B 3 " (cutoff:3.500A) Proline residue: B 16 - end of helix Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 49 through 60 Processing helix chain 'B' and resid 68 through 93 removed outlier: 3.760A pdb=" N LYS B 79 " --> pdb=" O ASP B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 110 Processing helix chain 'B' and resid 116 through 126 Processing helix chain 'B' and resid 126 through 143 removed outlier: 3.536A pdb=" N GLY B 130 " --> pdb=" O GLY B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 165 Processing helix chain 'B' and resid 167 through 171 removed outlier: 4.293A pdb=" N ALA B 170 " --> pdb=" O GLU B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 492 Processing helix chain 'B' and resid 494 through 514 Processing helix chain 'B' and resid 518 through 530 removed outlier: 4.214A pdb=" N LEU B 528 " --> pdb=" O SER B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 547 removed outlier: 3.514A pdb=" N GLN B 547 " --> pdb=" O PHE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 581 removed outlier: 4.262A pdb=" N GLY B 569 " --> pdb=" O ARG B 565 " (cutoff:3.500A) Proline residue: B 570 - end of helix Processing helix chain 'B' and resid 583 through 595 removed outlier: 4.004A pdb=" N ARG B 588 " --> pdb=" O GLY B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 610 removed outlier: 3.837A pdb=" N PHE B 603 " --> pdb=" O GLY B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 640 removed outlier: 3.551A pdb=" N LEU B 616 " --> pdb=" O HIS B 612 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LEU B 628 " --> pdb=" O MET B 624 " (cutoff:3.500A) Proline residue: B 629 - end of helix Processing helix chain 'A' and resid 4 through 30 Proline residue: A 16 - end of helix Processing helix chain 'A' and resid 35 through 60 removed outlier: 4.811A pdb=" N VAL A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Proline residue: A 52 - end of helix Processing helix chain 'A' and resid 68 through 93 removed outlier: 3.764A pdb=" N LYS A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 110 Processing helix chain 'A' and resid 116 through 126 Processing helix chain 'A' and resid 126 through 143 removed outlier: 3.542A pdb=" N GLY A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 165 Processing helix chain 'A' and resid 167 through 171 removed outlier: 4.268A pdb=" N ALA A 170 " --> pdb=" O GLU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 492 Processing helix chain 'A' and resid 494 through 514 Processing helix chain 'A' and resid 518 through 530 removed outlier: 4.208A pdb=" N LEU A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 547 removed outlier: 3.512A pdb=" N GLN A 547 " --> pdb=" O PHE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 581 removed outlier: 4.262A pdb=" N GLY A 569 " --> pdb=" O ARG A 565 " (cutoff:3.500A) Proline residue: A 570 - end of helix Processing helix chain 'A' and resid 583 through 595 removed outlier: 3.978A pdb=" N ARG A 588 " --> pdb=" O GLY A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 610 removed outlier: 3.845A pdb=" N PHE A 603 " --> pdb=" O GLY A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 640 removed outlier: 3.550A pdb=" N LEU A 616 " --> pdb=" O HIS A 612 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU A 628 " --> pdb=" O MET A 624 " (cutoff:3.500A) Proline residue: A 629 - end of helix Processing sheet with id=AA1, first strand: chain 'B' and resid 174 through 177 removed outlier: 6.225A pdb=" N SER B 174 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N VAL B 206 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LYS B 176 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N LYS B 208 " --> pdb=" O LYS B 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 174 through 177 removed outlier: 6.229A pdb=" N SER A 174 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL A 206 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LYS A 176 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N LYS A 208 " --> pdb=" O LYS A 176 " (cutoff:3.500A) 443 hydrogen bonds defined for protein. 1323 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: 2.68 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 6132 1.02 - 1.21: 8 1.21 - 1.41: 2426 1.41 - 1.61: 3560 1.61 - 1.81: 78 Bond restraints: 12204 Sorted by residual: bond pdb=" ND2 ASN A 112 " pdb="HD22 ASN A 112 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" ND2 ASN A 112 " pdb="HD21 ASN A 112 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" ND2 ASN B 112 " pdb="HD21 ASN B 112 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" ND2 ASN B 112 " pdb="HD22 ASN B 112 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" C12 E7O B 701 " pdb=" N11 E7O B 701 " ideal model delta sigma weight residual 1.347 1.458 -0.111 2.00e-02 2.50e+03 3.10e+01 ... (remaining 12199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 21409 1.33 - 2.65: 685 2.65 - 3.98: 48 3.98 - 5.30: 10 5.30 - 6.63: 8 Bond angle restraints: 22160 Sorted by residual: angle pdb=" N ASN B 112 " pdb=" CA ASN B 112 " pdb=" C ASN B 112 " ideal model delta sigma weight residual 108.41 102.31 6.10 1.61e+00 3.86e-01 1.43e+01 angle pdb=" N ASN A 112 " pdb=" CA ASN A 112 " pdb=" C ASN A 112 " ideal model delta sigma weight residual 108.41 102.38 6.03 1.61e+00 3.86e-01 1.40e+01 angle pdb=" N VAL A 173 " pdb=" CA VAL A 173 " pdb=" C VAL A 173 " ideal model delta sigma weight residual 113.71 111.37 2.34 9.50e-01 1.11e+00 6.09e+00 angle pdb=" N VAL B 173 " pdb=" CA VAL B 173 " pdb=" C VAL B 173 " ideal model delta sigma weight residual 113.71 111.40 2.31 9.50e-01 1.11e+00 5.91e+00 angle pdb=" N TYR A 145 " pdb=" CA TYR A 145 " pdb=" C TYR A 145 " ideal model delta sigma weight residual 111.36 108.85 2.51 1.09e+00 8.42e-01 5.31e+00 ... (remaining 22155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 5150 16.79 - 33.58: 403 33.58 - 50.37: 101 50.37 - 67.15: 54 67.15 - 83.94: 2 Dihedral angle restraints: 5710 sinusoidal: 3066 harmonic: 2644 Sorted by residual: dihedral pdb=" CA PHE A 49 " pdb=" C PHE A 49 " pdb=" N ALA A 50 " pdb=" CA ALA A 50 " ideal model delta harmonic sigma weight residual -180.00 -162.80 -17.20 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA PHE B 49 " pdb=" C PHE B 49 " pdb=" N ALA B 50 " pdb=" CA ALA B 50 " ideal model delta harmonic sigma weight residual -180.00 -162.95 -17.05 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CG ARG B 29 " pdb=" CD ARG B 29 " pdb=" NE ARG B 29 " pdb=" CZ ARG B 29 " ideal model delta sinusoidal sigma weight residual -180.00 -135.46 -44.54 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 5707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 765 0.038 - 0.076: 165 0.076 - 0.115: 54 0.115 - 0.153: 4 0.153 - 0.191: 2 Chirality restraints: 990 Sorted by residual: chirality pdb=" CA ASN B 112 " pdb=" N ASN B 112 " pdb=" C ASN B 112 " pdb=" CB ASN B 112 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.12e-01 chirality pdb=" CA ASN A 112 " pdb=" N ASN A 112 " pdb=" C ASN A 112 " pdb=" CB ASN A 112 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.90e-01 chirality pdb=" CA PRO A 16 " pdb=" N PRO A 16 " pdb=" C PRO A 16 " pdb=" CB PRO A 16 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.39e-01 ... (remaining 987 not shown) Planarity restraints: 1714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 112 " -0.080 2.00e-02 2.50e+03 7.86e-02 9.27e+01 pdb=" CG ASN B 112 " 0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN B 112 " 0.076 2.00e-02 2.50e+03 pdb=" ND2 ASN B 112 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN B 112 " 0.110 2.00e-02 2.50e+03 pdb="HD22 ASN B 112 " -0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 112 " -0.077 2.00e-02 2.50e+03 7.53e-02 8.51e+01 pdb=" CG ASN A 112 " 0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN A 112 " 0.073 2.00e-02 2.50e+03 pdb=" ND2 ASN A 112 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN A 112 " 0.106 2.00e-02 2.50e+03 pdb="HD22 ASN A 112 " -0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 569 " -0.032 5.00e-02 4.00e+02 4.79e-02 3.66e+00 pdb=" N PRO B 570 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 570 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 570 " -0.027 5.00e-02 4.00e+02 ... (remaining 1711 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 638 2.21 - 2.80: 24683 2.80 - 3.40: 33104 3.40 - 4.00: 42849 4.00 - 4.60: 67373 Nonbonded interactions: 168647 Sorted by model distance: nonbonded pdb=" O GLU B 178 " pdb="HH12 ARG B 489 " model vdw 1.607 2.450 nonbonded pdb=" HH TYR A 18 " pdb=" O MET A 624 " model vdw 1.607 2.450 nonbonded pdb=" O GLU A 178 " pdb="HH12 ARG A 489 " model vdw 1.608 2.450 nonbonded pdb=" HH TYR B 18 " pdb=" O MET B 624 " model vdw 1.609 2.450 nonbonded pdb=" O LEU B 23 " pdb=" HG SER B 27 " model vdw 1.615 2.450 ... (remaining 168642 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } 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: 1.220 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 13.370 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:8.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 6066 Z= 0.197 Angle : 0.565 6.626 8266 Z= 0.297 Chirality : 0.038 0.191 990 Planarity : 0.005 0.048 998 Dihedral : 13.100 83.944 2134 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.31), residues: 746 helix: 1.70 (0.22), residues: 560 sheet: -0.12 (0.79), residues: 42 loop : -0.65 (0.55), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 44 TYR 0.005 0.001 TYR B 635 PHE 0.007 0.001 PHE A 45 TRP 0.009 0.001 TRP A 506 HIS 0.002 0.001 HIS B 57 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 6066) covalent geometry : angle 0.56536 ( 8266) hydrogen bonds : bond 0.10268 ( 443) hydrogen bonds : angle 6.00124 ( 1323) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.8982 time to fit residues: 121.7005 Evaluate side-chains 84 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.0040 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.177381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.149763 restraints weight = 17380.766| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 1.32 r_work: 0.3551 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6066 Z= 0.207 Angle : 0.728 7.524 8266 Z= 0.371 Chirality : 0.042 0.141 990 Planarity : 0.007 0.076 998 Dihedral : 4.967 18.593 816 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.35 % Allowed : 8.15 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.31), residues: 746 helix: 1.39 (0.21), residues: 562 sheet: 0.14 (0.80), residues: 42 loop : -1.21 (0.54), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 207 TYR 0.013 0.002 TYR A 498 PHE 0.016 0.002 PHE B 56 TRP 0.018 0.002 TRP B 506 HIS 0.004 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 6066) covalent geometry : angle 0.72755 ( 8266) hydrogen bonds : bond 0.05054 ( 443) hydrogen bonds : angle 5.24441 ( 1323) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.298 Fit side-chains REVERT: B 21 MET cc_start: 0.7201 (ttp) cc_final: 0.6919 (ttp) REVERT: B 159 MET cc_start: 0.6963 (mtp) cc_final: 0.6706 (mtp) REVERT: A 21 MET cc_start: 0.7216 (ttp) cc_final: 0.6859 (ttp) REVERT: A 159 MET cc_start: 0.7024 (mtp) cc_final: 0.6785 (mtp) REVERT: A 517 MET cc_start: 0.6354 (OUTLIER) cc_final: 0.6116 (ttm) outliers start: 15 outliers final: 7 residues processed: 107 average time/residue: 0.7592 time to fit residues: 86.6396 Evaluate side-chains 85 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 626 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 52 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 522 GLN A 140 GLN A 522 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.177521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.147724 restraints weight = 17800.477| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.17 r_work: 0.3543 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.6406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6066 Z= 0.206 Angle : 0.690 6.281 8266 Z= 0.359 Chirality : 0.042 0.142 990 Planarity : 0.006 0.063 998 Dihedral : 6.223 36.044 816 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.51 % Allowed : 11.91 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.30), residues: 746 helix: 1.20 (0.21), residues: 570 sheet: -0.23 (0.70), residues: 42 loop : -1.32 (0.59), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 481 TYR 0.020 0.002 TYR B 498 PHE 0.008 0.002 PHE A 603 TRP 0.012 0.002 TRP A 506 HIS 0.006 0.002 HIS B 57 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 6066) covalent geometry : angle 0.68983 ( 8266) hydrogen bonds : bond 0.06597 ( 443) hydrogen bonds : angle 5.37046 ( 1323) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 585 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.7132 (t70) REVERT: B 624 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.6788 (tpt) REVERT: A 178 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6900 (mp0) REVERT: A 624 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.6693 (tpt) outliers start: 16 outliers final: 4 residues processed: 103 average time/residue: 0.7959 time to fit residues: 87.4102 Evaluate side-chains 89 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 585 ASP Chi-restraints excluded: chain B residue 624 MET Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 626 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 3 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.176899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.147469 restraints weight = 17634.591| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.17 r_work: 0.3554 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.7244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6066 Z= 0.178 Angle : 0.613 5.483 8266 Z= 0.315 Chirality : 0.040 0.169 990 Planarity : 0.006 0.051 998 Dihedral : 5.254 27.170 816 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.82 % Allowed : 12.38 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.31), residues: 746 helix: 1.30 (0.21), residues: 568 sheet: -0.11 (0.73), residues: 42 loop : -1.40 (0.56), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 207 TYR 0.006 0.001 TYR B 635 PHE 0.010 0.001 PHE A 45 TRP 0.011 0.002 TRP B 506 HIS 0.003 0.001 HIS B 57 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 6066) covalent geometry : angle 0.61318 ( 8266) hydrogen bonds : bond 0.05203 ( 443) hydrogen bonds : angle 5.14605 ( 1323) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 21 MET cc_start: 0.8399 (ttp) cc_final: 0.7841 (ttt) REVERT: B 520 ILE cc_start: 0.7277 (OUTLIER) cc_final: 0.6913 (mt) REVERT: B 624 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.6992 (tpt) REVERT: A 178 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6765 (mp0) REVERT: A 520 ILE cc_start: 0.7251 (OUTLIER) cc_final: 0.6895 (mt) REVERT: A 624 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7045 (tpt) outliers start: 18 outliers final: 7 residues processed: 100 average time/residue: 0.9496 time to fit residues: 100.3717 Evaluate side-chains 92 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 624 MET Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 626 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 31 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 0.0980 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 522 GLN A 522 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.178514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.148946 restraints weight = 17610.685| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.17 r_work: 0.3555 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.7518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6066 Z= 0.133 Angle : 0.532 6.530 8266 Z= 0.278 Chirality : 0.037 0.132 990 Planarity : 0.005 0.048 998 Dihedral : 4.935 23.069 816 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.88 % Allowed : 13.32 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.30), residues: 746 helix: 1.54 (0.21), residues: 564 sheet: -0.18 (0.72), residues: 42 loop : -1.17 (0.55), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 493 TYR 0.008 0.001 TYR B 635 PHE 0.008 0.001 PHE A 45 TRP 0.010 0.001 TRP A 506 HIS 0.002 0.001 HIS B 57 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 6066) covalent geometry : angle 0.53200 ( 8266) hydrogen bonds : bond 0.04654 ( 443) hydrogen bonds : angle 4.98422 ( 1323) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 MET cc_start: 0.8414 (ttp) cc_final: 0.7995 (ttt) REVERT: B 127 GLU cc_start: 0.6560 (mp0) cc_final: 0.6323 (mm-30) REVERT: B 624 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7094 (tpt) REVERT: A 21 MET cc_start: 0.8243 (ttp) cc_final: 0.7918 (ttt) REVERT: A 127 GLU cc_start: 0.6535 (mp0) cc_final: 0.6303 (mm-30) REVERT: A 178 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6489 (mp0) REVERT: A 624 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7068 (tpt) outliers start: 12 outliers final: 6 residues processed: 86 average time/residue: 0.9322 time to fit residues: 84.8873 Evaluate side-chains 85 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 624 MET Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 626 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3984 r_free = 0.3984 target = 0.176778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.147117 restraints weight = 17597.446| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 1.17 r_work: 0.3571 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.7944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6066 Z= 0.142 Angle : 0.541 5.903 8266 Z= 0.282 Chirality : 0.038 0.135 990 Planarity : 0.005 0.049 998 Dihedral : 4.890 22.847 816 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.88 % Allowed : 13.01 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.30), residues: 746 helix: 1.58 (0.21), residues: 564 sheet: -0.07 (0.73), residues: 42 loop : -1.20 (0.55), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 155 TYR 0.006 0.001 TYR B 635 PHE 0.007 0.001 PHE B 566 TRP 0.010 0.001 TRP A 506 HIS 0.002 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6066) covalent geometry : angle 0.54100 ( 8266) hydrogen bonds : bond 0.04660 ( 443) hydrogen bonds : angle 4.96417 ( 1323) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: B 21 MET cc_start: 0.8493 (ttp) cc_final: 0.8201 (ttt) REVERT: B 624 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7265 (tpt) REVERT: A 21 MET cc_start: 0.8367 (ttp) cc_final: 0.8157 (ttt) REVERT: A 178 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6285 (mp0) REVERT: A 624 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7298 (tpt) outliers start: 12 outliers final: 5 residues processed: 86 average time/residue: 0.9942 time to fit residues: 90.2008 Evaluate side-chains 81 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 624 MET Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 626 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 522 GLN A 522 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.174133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.144537 restraints weight = 17485.627| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.18 r_work: 0.3527 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.8450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6066 Z= 0.166 Angle : 0.582 8.437 8266 Z= 0.303 Chirality : 0.039 0.138 990 Planarity : 0.006 0.052 998 Dihedral : 5.284 28.476 816 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.45 % Allowed : 12.07 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.30), residues: 746 helix: 1.42 (0.21), residues: 566 sheet: -0.09 (0.72), residues: 42 loop : -1.33 (0.54), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 565 TYR 0.017 0.001 TYR A 498 PHE 0.009 0.001 PHE A 45 TRP 0.012 0.002 TRP A 506 HIS 0.004 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 6066) covalent geometry : angle 0.58179 ( 8266) hydrogen bonds : bond 0.05000 ( 443) hydrogen bonds : angle 5.09524 ( 1323) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.241 Fit side-chains REVERT: B 21 MET cc_start: 0.8543 (ttp) cc_final: 0.8219 (ttt) REVERT: B 127 GLU cc_start: 0.6693 (mp0) cc_final: 0.6461 (mm-30) REVERT: B 624 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7197 (tpt) REVERT: A 21 MET cc_start: 0.8447 (ttp) cc_final: 0.8036 (ttt) REVERT: A 127 GLU cc_start: 0.6658 (mp0) cc_final: 0.6443 (mm-30) REVERT: A 178 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6165 (mp0) REVERT: A 624 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7148 (tpt) outliers start: 22 outliers final: 7 residues processed: 95 average time/residue: 0.9988 time to fit residues: 99.8893 Evaluate side-chains 93 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 624 MET Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 626 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 36 optimal weight: 0.4980 chunk 54 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.177035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.147813 restraints weight = 17479.552| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.18 r_work: 0.3562 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.8572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6066 Z= 0.129 Angle : 0.544 8.635 8266 Z= 0.281 Chirality : 0.037 0.132 990 Planarity : 0.005 0.049 998 Dihedral : 4.806 21.302 816 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.04 % Allowed : 13.79 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.30), residues: 746 helix: 1.61 (0.21), residues: 564 sheet: -0.11 (0.72), residues: 42 loop : -1.24 (0.55), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 493 TYR 0.008 0.001 TYR B 635 PHE 0.008 0.001 PHE A 45 TRP 0.010 0.001 TRP A 506 HIS 0.001 0.001 HIS B 57 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 6066) covalent geometry : angle 0.54425 ( 8266) hydrogen bonds : bond 0.04493 ( 443) hydrogen bonds : angle 4.94637 ( 1323) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.294 Fit side-chains REVERT: B 21 MET cc_start: 0.8525 (ttp) cc_final: 0.8215 (ttt) REVERT: B 178 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6352 (mp0) REVERT: B 624 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7261 (tpt) REVERT: A 21 MET cc_start: 0.8465 (ttp) cc_final: 0.8230 (ttt) REVERT: A 178 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6061 (mp0) REVERT: A 624 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7239 (tpt) outliers start: 13 outliers final: 8 residues processed: 89 average time/residue: 0.9601 time to fit residues: 90.5712 Evaluate side-chains 92 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 624 MET Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 626 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 46 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 522 GLN A 522 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.173091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.143900 restraints weight = 17523.450| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.15 r_work: 0.3517 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.8883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6066 Z= 0.194 Angle : 0.617 9.479 8266 Z= 0.323 Chirality : 0.040 0.139 990 Planarity : 0.006 0.054 998 Dihedral : 5.665 33.928 816 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.82 % Allowed : 12.85 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.30), residues: 746 helix: 1.32 (0.21), residues: 564 sheet: -0.26 (0.72), residues: 42 loop : -1.38 (0.54), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 565 TYR 0.015 0.002 TYR A 498 PHE 0.010 0.002 PHE A 45 TRP 0.014 0.002 TRP A 506 HIS 0.003 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 6066) covalent geometry : angle 0.61745 ( 8266) hydrogen bonds : bond 0.05358 ( 443) hydrogen bonds : angle 5.24425 ( 1323) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.323 Fit side-chains REVERT: B 21 MET cc_start: 0.8597 (ttp) cc_final: 0.8386 (ttt) REVERT: B 127 GLU cc_start: 0.6735 (mp0) cc_final: 0.6502 (mm-30) REVERT: B 178 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.6260 (mp0) REVERT: B 624 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7178 (tpt) REVERT: A 21 MET cc_start: 0.8521 (ttp) cc_final: 0.8106 (ttt) REVERT: A 127 GLU cc_start: 0.6722 (mp0) cc_final: 0.6514 (mm-30) REVERT: A 178 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.5936 (mp0) REVERT: A 624 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7174 (tpt) outliers start: 18 outliers final: 9 residues processed: 94 average time/residue: 0.9352 time to fit residues: 92.9573 Evaluate side-chains 97 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 624 MET Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 626 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 0.0870 chunk 3 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 0.2980 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 = 0.3976 r_free = 0.3976 target = 0.175803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.146044 restraints weight = 17446.670| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.15 r_work: 0.3569 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.8943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6066 Z= 0.116 Angle : 0.533 8.095 8266 Z= 0.277 Chirality : 0.037 0.129 990 Planarity : 0.005 0.048 998 Dihedral : 4.566 17.496 816 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.94 % Allowed : 14.58 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.31), residues: 746 helix: 1.76 (0.21), residues: 560 sheet: -0.05 (0.75), residues: 42 loop : -1.29 (0.54), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 565 TYR 0.008 0.001 TYR B 635 PHE 0.009 0.001 PHE A 175 TRP 0.009 0.001 TRP B 144 HIS 0.002 0.001 HIS B 57 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 6066) covalent geometry : angle 0.53279 ( 8266) hydrogen bonds : bond 0.04205 ( 443) hydrogen bonds : angle 4.90824 ( 1323) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 21 MET cc_start: 0.8576 (ttp) cc_final: 0.8354 (ttt) REVERT: B 70 ARG cc_start: 0.7843 (mmm-85) cc_final: 0.7612 (mmm-85) REVERT: B 163 GLU cc_start: 0.5150 (tm-30) cc_final: 0.4938 (tm-30) REVERT: B 624 MET cc_start: 0.8004 (tpt) cc_final: 0.7311 (tpt) REVERT: A 70 ARG cc_start: 0.7822 (mmm-85) cc_final: 0.7593 (mmm-85) REVERT: A 178 GLU cc_start: 0.6629 (OUTLIER) cc_final: 0.5899 (mp0) REVERT: A 624 MET cc_start: 0.8179 (tpt) cc_final: 0.7203 (tpt) outliers start: 6 outliers final: 5 residues processed: 84 average time/residue: 0.9263 time to fit residues: 82.4610 Evaluate side-chains 88 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 626 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 39 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.173275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.143427 restraints weight = 17363.237| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.16 r_work: 0.3516 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.9053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6066 Z= 0.149 Angle : 0.571 10.366 8266 Z= 0.293 Chirality : 0.038 0.135 990 Planarity : 0.005 0.051 998 Dihedral : 4.838 20.779 816 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.94 % Allowed : 14.89 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.30), residues: 746 helix: 1.63 (0.21), residues: 564 sheet: -0.07 (0.75), residues: 42 loop : -1.27 (0.55), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 70 TYR 0.010 0.001 TYR A 498 PHE 0.008 0.001 PHE B 566 TRP 0.010 0.001 TRP A 506 HIS 0.002 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 6066) covalent geometry : angle 0.57069 ( 8266) hydrogen bonds : bond 0.04648 ( 443) hydrogen bonds : angle 5.01371 ( 1323) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3982.23 seconds wall clock time: 67 minutes 58.04 seconds (4078.04 seconds total)