Starting phenix.real_space_refine on Tue Mar 3 13:13:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ezv_31391/03_2026/7ezv_31391.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ezv_31391/03_2026/7ezv_31391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ezv_31391/03_2026/7ezv_31391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ezv_31391/03_2026/7ezv_31391.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ezv_31391/03_2026/7ezv_31391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ezv_31391/03_2026/7ezv_31391.map" } resolution = 3.3 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= 0.002 sd= 0.049 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 22 5.16 5 C 3131 2.51 5 N 835 2.21 5 O 949 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4937 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1465 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "H" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 912 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 805 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "M" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 927 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "N" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Time building chain proxies: 1.13, per 1000 atoms: 0.23 Number of scatterers: 4937 At special positions: 0 Unit cell: (99.36, 90.72, 98.28, 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 22 16.00 O 949 8.00 N 835 7.00 C 3131 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 101 " - pdb=" SG CYS M 106 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 89 " distance=2.03 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: 0.45 Conformation dependent library (CDL) restraints added in 451.6 milliseconds 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1152 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 13 sheets defined 9.3% alpha, 34.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 385 through 390 removed outlier: 4.025A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.752A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.698A pdb=" N VAL L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 31 Processing helix chain 'M' and resid 73 through 76 Processing helix chain 'M' and resid 101 through 105 removed outlier: 3.778A pdb=" N GLY M 104 " --> pdb=" O CYS M 101 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR M 105 " --> pdb=" O SER M 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 101 through 105' Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.501A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA5, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AA8, first strand: chain 'L' and resid 44 through 48 removed outlier: 6.378A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 3 through 5 Processing sheet with id=AB1, first strand: chain 'M' and resid 57 through 60 removed outlier: 6.725A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N TRP M 50 " --> pdb=" O VAL M 34 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 57 through 60 removed outlier: 6.725A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N TRP M 50 " --> pdb=" O VAL M 34 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 5 through 6 Processing sheet with id=AB4, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.029A pdb=" N LEU N 11 " --> pdb=" O GLU N 106 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR N 103 " --> pdb=" O TYR N 87 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) 175 hydrogen bonds defined for protein. 411 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: 0.85 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 867 1.32 - 1.45: 1451 1.45 - 1.57: 2715 1.57 - 1.69: 0 1.69 - 1.81: 27 Bond restraints: 5060 Sorted by residual: bond pdb=" CA ALA A 475 " pdb=" CB ALA A 475 " ideal model delta sigma weight residual 1.532 1.490 0.042 1.53e-02 4.27e+03 7.58e+00 bond pdb=" N THR A 478 " pdb=" CA THR A 478 " ideal model delta sigma weight residual 1.453 1.483 -0.030 1.16e-02 7.43e+03 6.64e+00 bond pdb=" C PRO A 479 " pdb=" O PRO A 479 " ideal model delta sigma weight residual 1.233 1.205 0.028 1.16e-02 7.43e+03 5.93e+00 bond pdb=" CA SER A 477 " pdb=" CB SER A 477 " ideal model delta sigma weight residual 1.530 1.491 0.038 1.63e-02 3.76e+03 5.56e+00 bond pdb=" N ASN A 481 " pdb=" CA ASN A 481 " ideal model delta sigma weight residual 1.460 1.488 -0.028 1.39e-02 5.18e+03 3.97e+00 ... (remaining 5055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 6660 1.80 - 3.60: 176 3.60 - 5.40: 32 5.40 - 7.21: 3 7.21 - 9.01: 2 Bond angle restraints: 6873 Sorted by residual: angle pdb=" C PRO A 479 " pdb=" CA PRO A 479 " pdb=" CB PRO A 479 " ideal model delta sigma weight residual 111.46 105.43 6.03 1.29e+00 6.01e-01 2.18e+01 angle pdb=" C GLY A 482 " pdb=" N VAL A 483 " pdb=" CA VAL A 483 " ideal model delta sigma weight residual 123.13 118.95 4.18 1.34e+00 5.57e-01 9.74e+00 angle pdb=" CA SER A 477 " pdb=" C SER A 477 " pdb=" O SER A 477 " ideal model delta sigma weight residual 120.55 117.27 3.28 1.07e+00 8.73e-01 9.39e+00 angle pdb=" C ALA L 51 " pdb=" N SER L 52 " pdb=" CA SER L 52 " ideal model delta sigma weight residual 121.54 127.33 -5.79 1.91e+00 2.74e-01 9.20e+00 angle pdb=" N ALA A 475 " pdb=" CA ALA A 475 " pdb=" C ALA A 475 " ideal model delta sigma weight residual 113.41 109.71 3.70 1.22e+00 6.72e-01 9.18e+00 ... (remaining 6868 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 2692 17.47 - 34.93: 233 34.93 - 52.40: 45 52.40 - 69.87: 7 69.87 - 87.33: 3 Dihedral angle restraints: 2980 sinusoidal: 1160 harmonic: 1820 Sorted by residual: dihedral pdb=" CB CYS N 23 " pdb=" SG CYS N 23 " pdb=" SG CYS N 89 " pdb=" CB CYS N 89 " ideal model delta sinusoidal sigma weight residual 93.00 156.07 -63.07 1 1.00e+01 1.00e-02 5.25e+01 dihedral pdb=" CA ALA L 94 " pdb=" C ALA L 94 " pdb=" N PRO L 95 " pdb=" CA PRO L 95 " ideal model delta harmonic sigma weight residual -180.00 -143.91 -36.09 0 5.00e+00 4.00e-02 5.21e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 147.80 -54.80 1 1.00e+01 1.00e-02 4.07e+01 ... (remaining 2977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 521 0.040 - 0.081: 144 0.081 - 0.121: 56 0.121 - 0.162: 14 0.162 - 0.202: 3 Chirality restraints: 738 Sorted by residual: chirality pdb=" CA PRO L 95 " pdb=" N PRO L 95 " pdb=" C PRO L 95 " pdb=" CB PRO L 95 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA ILE M 51 " pdb=" N ILE M 51 " pdb=" C ILE M 51 " pdb=" CB ILE M 51 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.11e-01 chirality pdb=" CA CYS A 480 " pdb=" N CYS A 480 " pdb=" C CYS A 480 " pdb=" CB CYS A 480 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.68e-01 ... (remaining 735 not shown) Planarity restraints: 883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA L 94 " -0.089 5.00e-02 4.00e+02 1.36e-01 2.96e+01 pdb=" N PRO L 95 " 0.235 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.076 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 65 " 0.120 9.50e-02 1.11e+02 5.45e-02 2.48e+00 pdb=" NE ARG L 65 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG L 65 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG L 65 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG L 65 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU N 80 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.48e+00 pdb=" N PRO N 81 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO N 81 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO N 81 " -0.022 5.00e-02 4.00e+02 ... (remaining 880 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 56 2.61 - 3.18: 4302 3.18 - 3.75: 7412 3.75 - 4.33: 10832 4.33 - 4.90: 18369 Nonbonded interactions: 40971 Sorted by model distance: nonbonded pdb=" OG1 THR M 28 " pdb=" O CYS M 101 " model vdw 2.034 3.040 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.173 3.040 nonbonded pdb=" NH2 ARG A 346 " pdb=" OD2 ASP H 54 " model vdw 2.248 3.120 nonbonded pdb=" OD1 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.252 3.040 nonbonded pdb=" OD2 ASP M 73 " pdb=" OG1 THR M 76 " model vdw 2.290 3.040 ... (remaining 40966 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.170 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 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 : 0.005 0.049 5068 Z= 0.241 Angle : 0.714 9.008 6889 Z= 0.395 Chirality : 0.047 0.202 738 Planarity : 0.007 0.136 883 Dihedral : 13.537 87.335 1804 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.36 % Favored : 91.32 % Rotamer: Outliers : 0.75 % Allowed : 0.75 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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 (0.33), residues: 622 helix: -3.09 (0.74), residues: 27 sheet: -0.21 (0.33), residues: 253 loop : -0.69 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 65 TYR 0.015 0.002 TYR L 91 PHE 0.018 0.002 PHE H 24 TRP 0.013 0.001 TRP M 36 HIS 0.006 0.004 HIS M 100 Details of bonding type rmsd covalent geometry : bond 0.00503 ( 5060) covalent geometry : angle 0.71208 ( 6873) SS BOND : bond 0.00414 ( 8) SS BOND : angle 1.29333 ( 16) hydrogen bonds : bond 0.14817 ( 157) hydrogen bonds : angle 7.89702 ( 411) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 101 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: L 90 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8752 (pp30) REVERT: N 101 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7772 (pp30) outliers start: 4 outliers final: 0 residues processed: 104 average time/residue: 0.1148 time to fit residues: 14.1879 Evaluate side-chains 88 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain N residue 101 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN M 100 HIS N 101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.071140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.059680 restraints weight = 13964.168| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.72 r_work: 0.2919 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5068 Z= 0.168 Angle : 0.643 9.001 6889 Z= 0.338 Chirality : 0.045 0.155 738 Planarity : 0.005 0.041 883 Dihedral : 6.047 43.643 709 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.07 % Favored : 92.77 % Rotamer: Outliers : 1.87 % Allowed : 9.70 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: -1.01 (0.33), residues: 622 helix: -2.98 (0.84), residues: 27 sheet: -0.05 (0.33), residues: 249 loop : -0.91 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 65 TYR 0.013 0.001 TYR M 107 PHE 0.013 0.001 PHE H 24 TRP 0.008 0.001 TRP N 36 HIS 0.003 0.002 HIS M 100 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 5060) covalent geometry : angle 0.63123 ( 6873) SS BOND : bond 0.00252 ( 8) SS BOND : angle 2.66742 ( 16) hydrogen bonds : bond 0.03452 ( 157) hydrogen bonds : angle 5.88285 ( 411) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8684 (mt-10) REVERT: A 408 ARG cc_start: 0.8789 (mtm110) cc_final: 0.8474 (ptp-110) REVERT: M 27 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.7308 (m-80) REVERT: M 73 ASP cc_start: 0.7608 (t0) cc_final: 0.7141 (t0) REVERT: M 80 TYR cc_start: 0.8608 (m-80) cc_final: 0.8215 (m-10) REVERT: N 104 LYS cc_start: 0.7581 (tmmt) cc_final: 0.7292 (ttpp) outliers start: 10 outliers final: 3 residues processed: 103 average time/residue: 0.1039 time to fit residues: 12.8853 Evaluate side-chains 88 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 27 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 4 optimal weight: 3.9990 chunk 30 optimal weight: 0.0980 chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 55 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN L 38 GLN M 39 GLN N 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.072170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.060651 restraints weight = 13945.389| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.75 r_work: 0.2941 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5068 Z= 0.126 Angle : 0.585 6.209 6889 Z= 0.308 Chirality : 0.045 0.221 738 Planarity : 0.004 0.042 883 Dihedral : 5.332 36.770 703 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.40 % Favored : 92.44 % Rotamer: Outliers : 2.43 % Allowed : 10.63 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: -0.87 (0.33), residues: 622 helix: -2.98 (0.78), residues: 27 sheet: 0.05 (0.33), residues: 250 loop : -0.80 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 65 TYR 0.017 0.001 TYR M 107 PHE 0.011 0.001 PHE H 24 TRP 0.007 0.001 TRP M 47 HIS 0.000 0.000 HIS M 100 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 5060) covalent geometry : angle 0.58119 ( 6873) SS BOND : bond 0.00289 ( 8) SS BOND : angle 1.46986 ( 16) hydrogen bonds : bond 0.03128 ( 157) hydrogen bonds : angle 5.50855 ( 411) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8918 (ttmm) cc_final: 0.8652 (ptmm) REVERT: A 408 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8389 (ptp-110) REVERT: H 54 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8164 (t70) REVERT: M 73 ASP cc_start: 0.7670 (t0) cc_final: 0.7263 (t0) REVERT: M 80 TYR cc_start: 0.8574 (m-80) cc_final: 0.8219 (m-10) REVERT: N 104 LYS cc_start: 0.7641 (tmmt) cc_final: 0.7314 (ttpp) outliers start: 13 outliers final: 4 residues processed: 95 average time/residue: 0.1070 time to fit residues: 12.1091 Evaluate side-chains 87 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 56 optimal weight: 0.0870 chunk 14 optimal weight: 3.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- 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 = 0.3284 r_free = 0.3284 target = 0.071291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.059790 restraints weight = 13891.532| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.71 r_work: 0.2921 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 5068 Z= 0.149 Angle : 0.590 6.885 6889 Z= 0.311 Chirality : 0.045 0.175 738 Planarity : 0.004 0.044 883 Dihedral : 5.211 26.374 703 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.91 % Favored : 92.93 % Rotamer: Outliers : 2.43 % Allowed : 12.50 % Favored : 85.07 % 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: -0.85 (0.33), residues: 622 helix: -2.95 (0.80), residues: 26 sheet: 0.01 (0.33), residues: 251 loop : -0.77 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 65 TYR 0.014 0.001 TYR L 91 PHE 0.010 0.001 PHE H 24 TRP 0.007 0.001 TRP N 36 HIS 0.000 0.000 HIS M 100 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 5060) covalent geometry : angle 0.58866 ( 6873) SS BOND : bond 0.00178 ( 8) SS BOND : angle 1.13090 ( 16) hydrogen bonds : bond 0.03030 ( 157) hydrogen bonds : angle 5.44926 ( 411) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8379 (ptp-110) REVERT: H 54 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8193 (t70) REVERT: M 27 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.7049 (m-80) REVERT: M 73 ASP cc_start: 0.7860 (t0) cc_final: 0.7457 (t0) REVERT: M 80 TYR cc_start: 0.8562 (m-80) cc_final: 0.8248 (m-10) outliers start: 13 outliers final: 6 residues processed: 87 average time/residue: 0.1119 time to fit residues: 11.6069 Evaluate side-chains 89 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 79 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.070314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.058675 restraints weight = 14110.572| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.73 r_work: 0.2891 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5068 Z= 0.167 Angle : 0.601 6.805 6889 Z= 0.316 Chirality : 0.045 0.175 738 Planarity : 0.004 0.044 883 Dihedral : 5.208 24.659 703 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.72 % Favored : 92.12 % Rotamer: Outliers : 3.36 % Allowed : 12.69 % Favored : 83.96 % 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: -0.86 (0.33), residues: 622 helix: -2.85 (0.83), residues: 26 sheet: 0.04 (0.34), residues: 249 loop : -0.81 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 65 TYR 0.016 0.001 TYR L 91 PHE 0.009 0.001 PHE H 24 TRP 0.011 0.001 TRP H 47 HIS 0.000 0.000 HIS M 100 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 5060) covalent geometry : angle 0.59986 ( 6873) SS BOND : bond 0.00160 ( 8) SS BOND : angle 0.89286 ( 16) hydrogen bonds : bond 0.03071 ( 157) hydrogen bonds : angle 5.45438 ( 411) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 LYS cc_start: 0.9038 (ttmm) cc_final: 0.8770 (ttpp) REVERT: A 408 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8413 (ptp-110) REVERT: A 420 ASP cc_start: 0.8683 (m-30) cc_final: 0.8461 (m-30) REVERT: H 54 ASP cc_start: 0.8744 (OUTLIER) cc_final: 0.8248 (t70) REVERT: M 27 PHE cc_start: 0.8090 (OUTLIER) cc_final: 0.7132 (m-80) REVERT: M 73 ASP cc_start: 0.7897 (t0) cc_final: 0.7493 (t0) REVERT: M 80 TYR cc_start: 0.8572 (m-80) cc_final: 0.8268 (m-10) outliers start: 18 outliers final: 11 residues processed: 93 average time/residue: 0.1086 time to fit residues: 12.1931 Evaluate side-chains 93 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 79 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN L 27 GLN L 38 GLN M 39 GLN N 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.069312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.057612 restraints weight = 14235.377| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.72 r_work: 0.2864 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5068 Z= 0.212 Angle : 0.632 7.368 6889 Z= 0.332 Chirality : 0.046 0.159 738 Planarity : 0.005 0.043 883 Dihedral : 5.320 24.357 703 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.88 % Favored : 91.96 % Rotamer: Outliers : 3.36 % Allowed : 12.87 % Favored : 83.77 % 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: -0.91 (0.33), residues: 622 helix: -3.00 (0.78), residues: 26 sheet: -0.07 (0.33), residues: 256 loop : -0.77 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 65 TYR 0.018 0.002 TYR M 107 PHE 0.009 0.001 PHE N 34 TRP 0.010 0.001 TRP H 47 HIS 0.000 0.000 HIS M 100 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 5060) covalent geometry : angle 0.62957 ( 6873) SS BOND : bond 0.00210 ( 8) SS BOND : angle 1.31127 ( 16) hydrogen bonds : bond 0.03206 ( 157) hydrogen bonds : angle 5.52348 ( 411) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8397 (ptp-110) REVERT: A 420 ASP cc_start: 0.8682 (m-30) cc_final: 0.8445 (m-30) REVERT: M 19 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8442 (mmm160) REVERT: M 27 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7161 (m-80) REVERT: M 73 ASP cc_start: 0.7902 (t0) cc_final: 0.7533 (t0) outliers start: 18 outliers final: 13 residues processed: 88 average time/residue: 0.1205 time to fit residues: 12.6312 Evaluate side-chains 95 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 19 ARG Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 79 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 7 optimal weight: 0.0370 chunk 49 optimal weight: 0.0870 chunk 59 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.0980 chunk 36 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN L 38 GLN M 39 GLN N 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.072458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.061087 restraints weight = 13922.779| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.68 r_work: 0.2955 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 5068 Z= 0.108 Angle : 0.577 6.329 6889 Z= 0.304 Chirality : 0.044 0.150 738 Planarity : 0.005 0.048 883 Dihedral : 4.920 24.632 703 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.75 % Favored : 93.09 % Rotamer: Outliers : 2.61 % Allowed : 14.37 % Favored : 83.02 % 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: -0.76 (0.34), residues: 622 helix: -2.96 (0.79), residues: 26 sheet: -0.11 (0.34), residues: 261 loop : -0.53 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 65 TYR 0.015 0.001 TYR M 107 PHE 0.010 0.001 PHE N 34 TRP 0.008 0.001 TRP H 83 HIS 0.000 0.000 HIS M 100 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 5060) covalent geometry : angle 0.57633 ( 6873) SS BOND : bond 0.00174 ( 8) SS BOND : angle 0.84792 ( 16) hydrogen bonds : bond 0.02788 ( 157) hydrogen bonds : angle 5.21772 ( 411) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8331 (mt-10) REVERT: A 408 ARG cc_start: 0.8773 (mtm110) cc_final: 0.8399 (ptp-110) REVERT: A 420 ASP cc_start: 0.8650 (m-30) cc_final: 0.8395 (m-30) REVERT: A 468 ILE cc_start: 0.9423 (pt) cc_final: 0.9119 (mt) REVERT: H 48 MET cc_start: 0.8785 (mtp) cc_final: 0.8510 (mtt) REVERT: H 54 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8176 (t70) REVERT: M 73 ASP cc_start: 0.7881 (t0) cc_final: 0.7523 (t0) REVERT: M 80 TYR cc_start: 0.8334 (m-80) cc_final: 0.7951 (m-10) outliers start: 14 outliers final: 9 residues processed: 88 average time/residue: 0.1076 time to fit residues: 11.2648 Evaluate side-chains 88 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 100 HIS Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 40 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 44 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.070279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.058742 restraints weight = 14124.383| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.69 r_work: 0.2894 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5068 Z= 0.179 Angle : 0.612 6.699 6889 Z= 0.322 Chirality : 0.045 0.156 738 Planarity : 0.005 0.053 883 Dihedral : 5.091 24.016 703 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.88 % Favored : 91.96 % Rotamer: Outliers : 3.36 % Allowed : 14.18 % Favored : 82.46 % 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: -0.82 (0.34), residues: 622 helix: -3.00 (0.79), residues: 26 sheet: -0.11 (0.34), residues: 252 loop : -0.60 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 65 TYR 0.018 0.001 TYR L 91 PHE 0.008 0.001 PHE N 34 TRP 0.010 0.001 TRP H 47 HIS 0.000 0.000 HIS M 100 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 5060) covalent geometry : angle 0.61143 ( 6873) SS BOND : bond 0.00129 ( 8) SS BOND : angle 0.93936 ( 16) hydrogen bonds : bond 0.03100 ( 157) hydrogen bonds : angle 5.33466 ( 411) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8798 (mtm110) cc_final: 0.8383 (ptp-110) REVERT: A 420 ASP cc_start: 0.8677 (m-30) cc_final: 0.8414 (m-30) REVERT: A 468 ILE cc_start: 0.9451 (pt) cc_final: 0.9109 (mt) REVERT: M 27 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.6957 (m-80) REVERT: M 73 ASP cc_start: 0.7886 (t0) cc_final: 0.7540 (t0) outliers start: 18 outliers final: 13 residues processed: 86 average time/residue: 0.1200 time to fit residues: 12.2279 Evaluate side-chains 91 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 3 optimal weight: 4.9990 chunk 34 optimal weight: 0.0050 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 29 optimal weight: 0.0980 chunk 59 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- 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 = 0.3279 r_free = 0.3279 target = 0.071118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.059775 restraints weight = 13927.049| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.66 r_work: 0.2922 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5068 Z= 0.137 Angle : 0.610 6.575 6889 Z= 0.320 Chirality : 0.044 0.154 738 Planarity : 0.005 0.056 883 Dihedral : 4.998 25.378 703 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.07 % Favored : 92.77 % Rotamer: Outliers : 2.43 % Allowed : 15.30 % Favored : 82.28 % 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: -0.75 (0.34), residues: 622 helix: -3.02 (0.78), residues: 26 sheet: -0.11 (0.34), residues: 266 loop : -0.52 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 65 TYR 0.017 0.001 TYR M 107 PHE 0.009 0.001 PHE N 34 TRP 0.009 0.001 TRP H 47 HIS 0.001 0.001 HIS M 100 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 5060) covalent geometry : angle 0.60901 ( 6873) SS BOND : bond 0.00144 ( 8) SS BOND : angle 0.79743 ( 16) hydrogen bonds : bond 0.02922 ( 157) hydrogen bonds : angle 5.25440 ( 411) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8775 (mtm110) cc_final: 0.8376 (ptp-110) REVERT: A 420 ASP cc_start: 0.8665 (m-30) cc_final: 0.8450 (m-30) REVERT: A 468 ILE cc_start: 0.9439 (pt) cc_final: 0.9104 (mt) REVERT: M 19 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8246 (mmm160) REVERT: M 27 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.6860 (m-80) REVERT: M 73 ASP cc_start: 0.7887 (t0) cc_final: 0.7556 (t0) outliers start: 13 outliers final: 9 residues processed: 86 average time/residue: 0.1150 time to fit residues: 11.8212 Evaluate side-chains 87 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 19 ARG Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 44 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN M 39 GLN N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.068898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.057492 restraints weight = 14057.951| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.64 r_work: 0.2865 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5068 Z= 0.219 Angle : 0.655 6.556 6889 Z= 0.343 Chirality : 0.046 0.224 738 Planarity : 0.005 0.058 883 Dihedral : 5.379 25.168 703 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.20 % Favored : 91.64 % Rotamer: Outliers : 2.80 % Allowed : 14.55 % Favored : 82.65 % 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: -0.93 (0.34), residues: 622 helix: -3.13 (0.74), residues: 27 sheet: -0.18 (0.34), residues: 257 loop : -0.68 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 65 TYR 0.021 0.002 TYR L 91 PHE 0.008 0.002 PHE N 63 TRP 0.011 0.001 TRP H 47 HIS 0.001 0.001 HIS M 100 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 5060) covalent geometry : angle 0.65353 ( 6873) SS BOND : bond 0.00149 ( 8) SS BOND : angle 1.01829 ( 16) hydrogen bonds : bond 0.03220 ( 157) hydrogen bonds : angle 5.45818 ( 411) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8792 (mtm110) cc_final: 0.8382 (ptp-110) REVERT: A 420 ASP cc_start: 0.8651 (m-30) cc_final: 0.8412 (m-30) REVERT: M 19 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8305 (mmm160) REVERT: M 27 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.6967 (m-80) REVERT: M 73 ASP cc_start: 0.7902 (t0) cc_final: 0.7569 (t0) outliers start: 15 outliers final: 10 residues processed: 87 average time/residue: 0.1196 time to fit residues: 12.3967 Evaluate side-chains 89 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 19 ARG Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 0.0870 chunk 22 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- 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 = 0.3283 r_free = 0.3283 target = 0.071215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.059867 restraints weight = 14128.708| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.67 r_work: 0.2927 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5068 Z= 0.136 Angle : 0.625 6.778 6889 Z= 0.328 Chirality : 0.044 0.156 738 Planarity : 0.005 0.057 883 Dihedral : 5.112 25.672 703 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.40 % Favored : 92.44 % Rotamer: Outliers : 2.61 % Allowed : 15.11 % Favored : 82.28 % 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: -0.77 (0.35), residues: 622 helix: -3.13 (0.76), residues: 26 sheet: -0.08 (0.34), residues: 271 loop : -0.57 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 65 TYR 0.023 0.001 TYR M 107 PHE 0.009 0.001 PHE N 34 TRP 0.009 0.001 TRP H 47 HIS 0.000 0.000 HIS M 100 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 5060) covalent geometry : angle 0.62236 ( 6873) SS BOND : bond 0.00238 ( 8) SS BOND : angle 1.29085 ( 16) hydrogen bonds : bond 0.02913 ( 157) hydrogen bonds : angle 5.26562 ( 411) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1266.83 seconds wall clock time: 22 minutes 27.81 seconds (1347.81 seconds total)