Starting phenix.real_space_refine on Thu Jul 24 01:53:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ezv_31391/07_2025/7ezv_31391.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ezv_31391/07_2025/7ezv_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ezv_31391/07_2025/7ezv_31391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ezv_31391/07_2025/7ezv_31391.map" model { file = "/net/cci-nas-00/data/ceres_data/7ezv_31391/07_2025/7ezv_31391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ezv_31391/07_2025/7ezv_31391.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 4.08, per 1000 atoms: 0.83 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: 1.46 Conformation dependent library (CDL) restraints added in 570.8 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: 0.68 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: 1.26 Time building geometry restraints manager: 1.47 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: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.680 Find NCS groups from input model: 0.070 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.013 0.001 TRP M 36 HIS 0.006 0.004 HIS M 100 PHE 0.018 0.002 PHE H 24 TYR 0.015 0.002 TYR L 91 ARG 0.014 0.001 ARG L 65 Details of bonding type rmsd hydrogen bonds : bond 0.14817 ( 157) hydrogen bonds : angle 7.89702 ( 411) SS BOND : bond 0.00414 ( 8) SS BOND : angle 1.29333 ( 16) covalent geometry : bond 0.00503 ( 5060) covalent geometry : angle 0.71208 ( 6873) *********************** 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 : 0.618 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: 0.2467 time to fit residues: 30.7972 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 : 0.629 ------------------------------------------------------------------------------- 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 51 optimal weight: 0.0040 chunk 46 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.5398 ------------------------------------------------------------------------------- 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 = 0.3250 r_free = 0.3250 target = 0.069786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.058290 restraints weight = 13905.247| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.69 r_work: 0.2883 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 5068 Z= 0.218 Angle : 0.673 9.675 6889 Z= 0.354 Chirality : 0.046 0.157 738 Planarity : 0.005 0.040 883 Dihedral : 6.223 44.368 709 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.56 % Favored : 92.28 % Rotamer: Outliers : 2.24 % Allowed : 9.70 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.33), residues: 622 helix: -3.00 (0.83), residues: 27 sheet: -0.21 (0.33), residues: 254 loop : -0.95 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 36 HIS 0.004 0.002 HIS M 100 PHE 0.015 0.002 PHE N 99 TYR 0.015 0.002 TYR L 91 ARG 0.007 0.001 ARG L 65 Details of bonding type rmsd hydrogen bonds : bond 0.03622 ( 157) hydrogen bonds : angle 5.95996 ( 411) SS BOND : bond 0.00338 ( 8) SS BOND : angle 2.82477 ( 16) covalent geometry : bond 0.00502 ( 5060) covalent geometry : angle 0.66008 ( 6873) *********************** 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 106 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8780 (mtm110) cc_final: 0.8480 (ptp-110) REVERT: M 27 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7389 (m-80) REVERT: M 73 ASP cc_start: 0.7573 (t0) cc_final: 0.7143 (t0) REVERT: M 80 TYR cc_start: 0.8639 (m-80) cc_final: 0.8292 (m-10) REVERT: N 104 LYS cc_start: 0.7696 (tmmt) cc_final: 0.7404 (ttpp) outliers start: 12 outliers final: 5 residues processed: 100 average time/residue: 0.2398 time to fit residues: 28.9362 Evaluate side-chains 91 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain N residue 20 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 45 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 0.0970 chunk 27 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.3295 r_free = 0.3295 target = 0.071749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.060276 restraints weight = 13907.145| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.72 r_work: 0.2934 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5068 Z= 0.129 Angle : 0.589 6.226 6889 Z= 0.311 Chirality : 0.045 0.217 738 Planarity : 0.005 0.043 883 Dihedral : 5.423 38.078 703 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.40 % Favored : 92.44 % Rotamer: Outliers : 2.05 % Allowed : 9.89 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.33), residues: 622 helix: -2.97 (1.01), residues: 20 sheet: 0.06 (0.33), residues: 248 loop : -0.92 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.000 0.000 HIS M 100 PHE 0.011 0.001 PHE H 24 TYR 0.018 0.001 TYR M 107 ARG 0.008 0.001 ARG L 65 Details of bonding type rmsd hydrogen bonds : bond 0.03144 ( 157) hydrogen bonds : angle 5.57363 ( 411) SS BOND : bond 0.00180 ( 8) SS BOND : angle 1.61111 ( 16) covalent geometry : bond 0.00296 ( 5060) covalent geometry : angle 0.58475 ( 6873) *********************** 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 106 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8924 (ttmm) cc_final: 0.8659 (ptmm) REVERT: A 408 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8376 (ptp-110) REVERT: H 54 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8188 (t70) REVERT: M 73 ASP cc_start: 0.7657 (t0) cc_final: 0.7270 (t0) REVERT: M 80 TYR cc_start: 0.8569 (m-80) cc_final: 0.8232 (m-10) REVERT: N 104 LYS cc_start: 0.7702 (tmmt) cc_final: 0.7396 (ttpp) outliers start: 11 outliers final: 3 residues processed: 100 average time/residue: 0.2494 time to fit residues: 30.0831 Evaluate side-chains 87 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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 20 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 45 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 29 optimal weight: 0.2980 chunk 2 optimal weight: 5.9990 chunk 24 optimal weight: 0.0060 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.8602 ------------------------------------------------------------------------------- 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 = 0.3278 r_free = 0.3278 target = 0.071019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.059577 restraints weight = 14137.729| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.67 r_work: 0.2919 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1953 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= 0.145 Angle : 0.594 6.751 6889 Z= 0.313 Chirality : 0.045 0.175 738 Planarity : 0.004 0.044 883 Dihedral : 5.247 27.854 703 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.07 % Favored : 92.77 % Rotamer: Outliers : 2.24 % Allowed : 12.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.34), residues: 622 helix: -2.39 (1.53), residues: 12 sheet: 0.04 (0.33), residues: 249 loop : -0.79 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 36 HIS 0.000 0.000 HIS M 100 PHE 0.010 0.001 PHE H 24 TYR 0.014 0.001 TYR L 91 ARG 0.009 0.001 ARG L 65 Details of bonding type rmsd hydrogen bonds : bond 0.03043 ( 157) hydrogen bonds : angle 5.44650 ( 411) SS BOND : bond 0.00210 ( 8) SS BOND : angle 1.15760 ( 16) covalent geometry : bond 0.00335 ( 5060) covalent geometry : angle 0.59206 ( 6873) *********************** 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: 12 poor density : 83 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8608 (mt-10) REVERT: A 408 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8357 (ptp-110) REVERT: H 54 ASP cc_start: 0.8673 (OUTLIER) cc_final: 0.8177 (t70) REVERT: M 27 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7018 (m-80) REVERT: M 73 ASP cc_start: 0.7861 (t0) cc_final: 0.7492 (t0) REVERT: M 80 TYR cc_start: 0.8519 (m-80) cc_final: 0.8207 (m-10) outliers start: 12 outliers final: 7 residues processed: 88 average time/residue: 0.2490 time to fit residues: 26.3797 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 : 0.610 ------------------------------------------------------------------------------- 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 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain M residue 105 THR 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 57 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3273 r_free = 0.3273 target = 0.070842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.059353 restraints weight = 13921.946| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.67 r_work: 0.2914 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5068 Z= 0.148 Angle : 0.585 6.771 6889 Z= 0.308 Chirality : 0.045 0.176 738 Planarity : 0.004 0.044 883 Dihedral : 5.132 24.336 703 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.56 % Favored : 92.28 % Rotamer: Outliers : 2.99 % Allowed : 13.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.34), residues: 622 helix: -2.68 (1.04), residues: 18 sheet: 0.01 (0.33), residues: 249 loop : -0.71 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 47 HIS 0.000 0.000 HIS M 100 PHE 0.010 0.001 PHE H 24 TYR 0.015 0.001 TYR L 91 ARG 0.009 0.001 ARG L 65 Details of bonding type rmsd hydrogen bonds : bond 0.02994 ( 157) hydrogen bonds : angle 5.39057 ( 411) SS BOND : bond 0.00139 ( 8) SS BOND : angle 0.93098 ( 16) covalent geometry : bond 0.00340 ( 5060) covalent geometry : angle 0.58416 ( 6873) *********************** 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 102 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 LYS cc_start: 0.9008 (ttmm) cc_final: 0.8698 (ptmm) REVERT: A 408 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8406 (ptp-110) REVERT: A 420 ASP cc_start: 0.8711 (m-30) cc_final: 0.8481 (m-30) REVERT: H 54 ASP cc_start: 0.8708 (OUTLIER) cc_final: 0.8186 (t70) REVERT: M 19 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8433 (mmm160) REVERT: M 27 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.7000 (m-80) REVERT: M 73 ASP cc_start: 0.7875 (t0) cc_final: 0.7503 (t0) REVERT: M 105 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.8045 (p) outliers start: 16 outliers final: 8 residues processed: 94 average time/residue: 0.2539 time to fit residues: 28.4530 Evaluate side-chains 93 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 L residue 20 THR Chi-restraints excluded: chain M residue 19 ARG Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain M residue 105 THR 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 42 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3255 r_free = 0.3255 target = 0.069957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.058353 restraints weight = 14006.060| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.72 r_work: 0.2886 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5068 Z= 0.189 Angle : 0.623 7.265 6889 Z= 0.327 Chirality : 0.045 0.162 738 Planarity : 0.004 0.043 883 Dihedral : 5.224 24.409 703 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.56 % Favored : 92.28 % Rotamer: Outliers : 3.92 % Allowed : 12.69 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.33), residues: 622 helix: -3.20 (0.75), residues: 27 sheet: -0.14 (0.33), residues: 258 loop : -0.70 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 36 HIS 0.000 0.000 HIS M 100 PHE 0.010 0.001 PHE H 24 TYR 0.018 0.001 TYR M 107 ARG 0.011 0.001 ARG L 65 Details of bonding type rmsd hydrogen bonds : bond 0.03121 ( 157) hydrogen bonds : angle 5.44130 ( 411) SS BOND : bond 0.00161 ( 8) SS BOND : angle 1.29095 ( 16) covalent geometry : bond 0.00432 ( 5060) covalent geometry : angle 0.62050 ( 6873) *********************** 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 103 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8384 (ptp-110) REVERT: A 420 ASP cc_start: 0.8738 (m-30) cc_final: 0.8509 (m-30) REVERT: A 468 ILE cc_start: 0.9460 (pt) cc_final: 0.9105 (mt) REVERT: H 54 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.8277 (t70) REVERT: M 27 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.7166 (m-80) REVERT: M 73 ASP cc_start: 0.7866 (t0) cc_final: 0.7528 (t0) REVERT: M 105 THR cc_start: 0.8255 (OUTLIER) cc_final: 0.7984 (p) outliers start: 21 outliers final: 12 residues processed: 91 average time/residue: 0.2512 time to fit residues: 27.8098 Evaluate side-chains 97 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 54 ASP 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 M residue 105 THR Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 75 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 15 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.3219 r_free = 0.3219 target = 0.068433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.056930 restraints weight = 13895.682| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.63 r_work: 0.2848 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 5068 Z= 0.253 Angle : 0.660 7.433 6889 Z= 0.348 Chirality : 0.046 0.149 738 Planarity : 0.005 0.046 883 Dihedral : 5.465 24.898 703 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.84 % Favored : 91.00 % Rotamer: Outliers : 3.54 % Allowed : 14.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.34), residues: 622 helix: -3.16 (0.77), residues: 27 sheet: -0.19 (0.33), residues: 261 loop : -0.72 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 36 HIS 0.001 0.001 HIS M 100 PHE 0.010 0.002 PHE N 34 TYR 0.020 0.002 TYR L 91 ARG 0.013 0.001 ARG L 65 Details of bonding type rmsd hydrogen bonds : bond 0.03356 ( 157) hydrogen bonds : angle 5.63780 ( 411) SS BOND : bond 0.00200 ( 8) SS BOND : angle 1.25669 ( 16) covalent geometry : bond 0.00574 ( 5060) covalent geometry : angle 0.65819 ( 6873) *********************** 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 99 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.663 Fit side-chains revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8422 (ptp-110) REVERT: M 19 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8383 (mmm160) REVERT: M 27 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.7295 (m-80) REVERT: M 73 ASP cc_start: 0.7874 (t0) cc_final: 0.7570 (t0) REVERT: M 105 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.8137 (p) outliers start: 19 outliers final: 11 residues processed: 88 average time/residue: 0.2934 time to fit residues: 31.0198 Evaluate side-chains 92 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 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 M residue 105 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 47 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 43 optimal weight: 0.4980 chunk 52 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 8 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 = 0.3240 r_free = 0.3240 target = 0.069330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.058011 restraints weight = 14093.997| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.65 r_work: 0.2879 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5068 Z= 0.182 Angle : 0.638 6.623 6889 Z= 0.334 Chirality : 0.045 0.149 738 Planarity : 0.005 0.051 883 Dihedral : 5.359 25.002 703 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.75 % Favored : 93.09 % Rotamer: Outliers : 3.17 % Allowed : 14.93 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.34), residues: 622 helix: -2.97 (0.81), residues: 26 sheet: -0.15 (0.33), residues: 267 loop : -0.72 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 47 HIS 0.002 0.001 HIS M 100 PHE 0.010 0.001 PHE H 24 TYR 0.017 0.001 TYR M 107 ARG 0.013 0.001 ARG L 65 Details of bonding type rmsd hydrogen bonds : bond 0.03173 ( 157) hydrogen bonds : angle 5.54300 ( 411) SS BOND : bond 0.00109 ( 8) SS BOND : angle 1.03071 ( 16) covalent geometry : bond 0.00416 ( 5060) covalent geometry : angle 0.63685 ( 6873) *********************** 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 99 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8603 (mt-10) REVERT: A 408 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8435 (ptp-110) REVERT: A 468 ILE cc_start: 0.9448 (pt) cc_final: 0.9087 (mt) REVERT: M 19 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8279 (mmm160) REVERT: M 27 PHE cc_start: 0.8267 (OUTLIER) cc_final: 0.7153 (m-80) REVERT: M 73 ASP cc_start: 0.7817 (t0) cc_final: 0.7507 (t0) REVERT: M 105 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.8070 (p) outliers start: 17 outliers final: 11 residues processed: 90 average time/residue: 0.3647 time to fit residues: 40.1476 Evaluate side-chains 95 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 5 VAL 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 M residue 105 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 19 optimal weight: 0.0060 chunk 57 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 52 optimal weight: 0.0050 overall best weight: 0.5612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.071336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.060085 restraints weight = 13901.902| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.66 r_work: 0.2929 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5068 Z= 0.119 Angle : 0.598 6.304 6889 Z= 0.312 Chirality : 0.044 0.154 738 Planarity : 0.005 0.054 883 Dihedral : 4.992 25.379 703 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.07 % Favored : 92.77 % Rotamer: Outliers : 2.43 % Allowed : 15.86 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.34), residues: 622 helix: -2.04 (1.19), residues: 18 sheet: -0.04 (0.34), residues: 256 loop : -0.52 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 83 HIS 0.001 0.000 HIS M 100 PHE 0.011 0.001 PHE H 24 TYR 0.018 0.001 TYR M 107 ARG 0.014 0.001 ARG L 65 Details of bonding type rmsd hydrogen bonds : bond 0.02903 ( 157) hydrogen bonds : angle 5.33629 ( 411) SS BOND : bond 0.00136 ( 8) SS BOND : angle 0.74861 ( 16) covalent geometry : bond 0.00272 ( 5060) covalent geometry : angle 0.59718 ( 6873) *********************** 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 101 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8581 (mt-10) REVERT: A 408 ARG cc_start: 0.8784 (mtm110) cc_final: 0.8400 (ptp-110) REVERT: A 468 ILE cc_start: 0.9419 (pt) cc_final: 0.9104 (mt) REVERT: M 19 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8251 (mmm160) REVERT: M 73 ASP cc_start: 0.7843 (t0) cc_final: 0.7523 (t0) REVERT: M 105 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7970 (p) outliers start: 13 outliers final: 8 residues processed: 93 average time/residue: 0.3672 time to fit residues: 41.6639 Evaluate side-chains 91 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain H residue 18 LEU 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 105 THR Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 7 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 0.0980 chunk 27 optimal weight: 3.9990 chunk 13 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 = 0.3291 r_free = 0.3291 target = 0.071641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.060362 restraints weight = 13978.671| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.68 r_work: 0.2939 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2569 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= 0.128 Angle : 0.622 6.349 6889 Z= 0.324 Chirality : 0.045 0.230 738 Planarity : 0.005 0.059 883 Dihedral : 4.991 25.085 703 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.75 % Favored : 93.09 % Rotamer: Outliers : 2.80 % Allowed : 15.67 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.35), residues: 622 helix: -2.06 (1.21), residues: 18 sheet: -0.10 (0.34), residues: 266 loop : -0.45 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 47 HIS 0.000 0.000 HIS M 100 PHE 0.010 0.001 PHE H 24 TYR 0.017 0.001 TYR M 107 ARG 0.014 0.001 ARG L 65 Details of bonding type rmsd hydrogen bonds : bond 0.02879 ( 157) hydrogen bonds : angle 5.22362 ( 411) SS BOND : bond 0.00119 ( 8) SS BOND : angle 1.34282 ( 16) covalent geometry : bond 0.00301 ( 5060) covalent geometry : angle 0.61889 ( 6873) ********************** 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 98 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.691 Fit side-chains REVERT: A 406 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8599 (mt-10) REVERT: A 408 ARG cc_start: 0.8782 (mtm110) cc_final: 0.8389 (ptp-110) REVERT: A 468 ILE cc_start: 0.9413 (pt) cc_final: 0.9119 (mt) REVERT: H 54 ASP cc_start: 0.8683 (OUTLIER) cc_final: 0.8246 (t70) REVERT: M 19 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8232 (mmm160) REVERT: M 27 PHE cc_start: 0.7710 (OUTLIER) cc_final: 0.6807 (m-80) REVERT: M 73 ASP cc_start: 0.7869 (t0) cc_final: 0.7535 (t0) REVERT: M 105 THR cc_start: 0.8153 (OUTLIER) cc_final: 0.7857 (p) outliers start: 15 outliers final: 8 residues processed: 90 average time/residue: 0.2855 time to fit residues: 31.0704 Evaluate side-chains 90 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 M residue 105 THR Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 M 100 HIS 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 = 0.071093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.059803 restraints weight = 14065.626| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.66 r_work: 0.2923 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5068 Z= 0.143 Angle : 0.626 6.450 6889 Z= 0.326 Chirality : 0.044 0.153 738 Planarity : 0.005 0.059 883 Dihedral : 5.057 25.161 703 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.23 % Favored : 92.60 % Rotamer: Outliers : 2.24 % Allowed : 16.79 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.34), residues: 622 helix: -1.91 (1.26), residues: 18 sheet: -0.04 (0.34), residues: 257 loop : -0.48 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 47 HIS 0.002 0.001 HIS M 100 PHE 0.009 0.001 PHE H 24 TYR 0.018 0.001 TYR L 91 ARG 0.014 0.001 ARG L 65 Details of bonding type rmsd hydrogen bonds : bond 0.02912 ( 157) hydrogen bonds : angle 5.23627 ( 411) SS BOND : bond 0.00177 ( 8) SS BOND : angle 1.20900 ( 16) covalent geometry : bond 0.00331 ( 5060) covalent geometry : angle 0.62403 ( 6873) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3827.47 seconds wall clock time: 69 minutes 27.25 seconds (4167.25 seconds total)