Starting phenix.real_space_refine on Sun Jun 8 09:02:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k9l_62193/06_2025/9k9l_62193.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k9l_62193/06_2025/9k9l_62193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k9l_62193/06_2025/9k9l_62193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k9l_62193/06_2025/9k9l_62193.map" model { file = "/net/cci-nas-00/data/ceres_data/9k9l_62193/06_2025/9k9l_62193.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k9l_62193/06_2025/9k9l_62193.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 242 5.49 5 S 8 5.16 5 C 5446 2.51 5 N 1855 2.21 5 O 2262 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9813 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 621 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "B" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 587 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "C" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 628 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "D" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 587 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "E" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 634 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain: "F" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 587 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "G" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 621 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "H" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 587 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "I" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2463 Classifications: {'DNA': 121} Link IDs: {'rna3p': 120} Chain: "J" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2498 Classifications: {'DNA': 121} Link IDs: {'rna3p': 120} Time building chain proxies: 6.46, per 1000 atoms: 0.66 Number of scatterers: 9813 At special positions: 0 Unit cell: (111.3, 118.72, 100.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 8 16.00 P 242 15.00 O 2262 8.00 N 1855 7.00 C 5446 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 579.6 milliseconds 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1126 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 7 sheets defined 79.8% alpha, 2.3% beta 120 base pairs and 184 stacking pairs defined. Time for finding SS restraints: 4.71 Creating SS restraints... Processing helix chain 'A' and resid 63 through 80 Processing helix chain 'A' and resid 87 through 116 Processing helix chain 'A' and resid 122 through 134 removed outlier: 3.781A pdb=" N VAL A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.517A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 63 through 79 removed outlier: 3.532A pdb=" N PHE C 67 " --> pdb=" O ARG C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 116 Processing helix chain 'C' and resid 122 through 134 removed outlier: 3.869A pdb=" N VAL C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN C 127 " --> pdb=" O PRO C 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 29 removed outlier: 3.551A pdb=" N ILE D 29 " --> pdb=" O ILE D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 41 Processing helix chain 'D' and resid 49 through 76 Processing helix chain 'D' and resid 82 through 94 Processing helix chain 'E' and resid 63 through 80 removed outlier: 3.504A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR E 79 " --> pdb=" O CYS E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 116 removed outlier: 3.502A pdb=" N ALA E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 134 removed outlier: 3.553A pdb=" N VAL E 126 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA E 129 " --> pdb=" O ASP E 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 63 through 79 removed outlier: 3.628A pdb=" N PHE G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 116 Processing helix chain 'G' and resid 122 through 134 Processing helix chain 'H' and resid 24 through 29 Processing helix chain 'H' and resid 30 through 41 Processing helix chain 'H' and resid 49 through 76 Processing helix chain 'H' and resid 82 through 94 Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 6.877A pdb=" N ASN A 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.705A pdb=" N LEU A 121 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 85 through 86 removed outlier: 6.652A pdb=" N ASN C 85 " --> pdb=" O VAL D 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 85 through 86 removed outlier: 6.763A pdb=" N ASN E 85 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 120 through 121 Processing sheet with id=AA6, first strand: chain 'G' and resid 85 through 86 removed outlier: 6.801A pdb=" N ASN G 85 " --> pdb=" O VAL H 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 120 through 121 360 hydrogen bonds defined for protein. 1050 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 312 hydrogen bonds 624 hydrogen bond angles 0 basepair planarities 120 basepair parallelities 184 stacking parallelities Total time for adding SS restraints: 3.99 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1883 1.33 - 1.45: 3461 1.45 - 1.57: 4650 1.57 - 1.69: 482 1.69 - 1.81: 12 Bond restraints: 10488 Sorted by residual: bond pdb=" N VAL D 81 " pdb=" CA VAL D 81 " ideal model delta sigma weight residual 1.460 1.494 -0.033 1.10e-02 8.26e+03 9.25e+00 bond pdb=" N ARG D 78 " pdb=" CA ARG D 78 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.33e-02 5.65e+03 5.65e+00 bond pdb=" N LYS D 79 " pdb=" CA LYS D 79 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.22e-02 6.72e+03 5.54e+00 bond pdb=" N GLU D 74 " pdb=" CA GLU D 74 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.47e+00 bond pdb=" N HIS D 75 " pdb=" CA HIS D 75 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.46e+00 ... (remaining 10483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 14548 1.46 - 2.91: 579 2.91 - 4.37: 49 4.37 - 5.82: 24 5.82 - 7.28: 3 Bond angle restraints: 15203 Sorted by residual: angle pdb=" CA LYS D 77 " pdb=" C LYS D 77 " pdb=" O LYS D 77 " ideal model delta sigma weight residual 121.84 118.24 3.60 1.16e+00 7.43e-01 9.61e+00 angle pdb=" N ALA D 76 " pdb=" CA ALA D 76 " pdb=" C ALA D 76 " ideal model delta sigma weight residual 113.20 109.47 3.73 1.21e+00 6.83e-01 9.52e+00 angle pdb=" CA THR D 80 " pdb=" CB THR D 80 " pdb=" OG1 THR D 80 " ideal model delta sigma weight residual 109.60 104.99 4.61 1.50e+00 4.44e-01 9.46e+00 angle pdb=" CA THR D 73 " pdb=" CB THR D 73 " pdb=" OG1 THR D 73 " ideal model delta sigma weight residual 109.60 105.13 4.47 1.50e+00 4.44e-01 8.88e+00 angle pdb=" CA ARG D 78 " pdb=" C ARG D 78 " pdb=" O ARG D 78 " ideal model delta sigma weight residual 121.58 118.31 3.27 1.16e+00 7.43e-01 7.94e+00 ... (remaining 15198 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.92: 4356 32.92 - 65.83: 1211 65.83 - 98.75: 35 98.75 - 131.67: 1 131.67 - 164.58: 3 Dihedral angle restraints: 5606 sinusoidal: 3873 harmonic: 1733 Sorted by residual: dihedral pdb=" C4' DC I 51 " pdb=" C3' DC I 51 " pdb=" O3' DC I 51 " pdb=" P DA I 52 " ideal model delta sinusoidal sigma weight residual 220.00 55.42 164.58 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DT I 14 " pdb=" C3' DT I 14 " pdb=" O3' DT I 14 " pdb=" P DT I 15 " ideal model delta sinusoidal sigma weight residual 220.00 59.11 160.89 1 3.50e+01 8.16e-04 1.52e+01 dihedral pdb=" C4' DC I -48 " pdb=" C3' DC I -48 " pdb=" O3' DC I -48 " pdb=" P DG I -47 " ideal model delta sinusoidal sigma weight residual 220.00 64.50 155.50 1 3.50e+01 8.16e-04 1.50e+01 ... (remaining 5603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 1714 0.109 - 0.217: 17 0.217 - 0.326: 1 0.326 - 0.434: 0 0.434 - 0.543: 1 Chirality restraints: 1733 Sorted by residual: chirality pdb=" P DC I 51 " pdb=" OP1 DC I 51 " pdb=" OP2 DC I 51 " pdb=" O5' DC I 51 " both_signs ideal model delta sigma weight residual True 2.35 -2.89 -0.54 2.00e-01 2.50e+01 7.37e+00 chirality pdb=" CB ILE H 46 " pdb=" CA ILE H 46 " pdb=" CG1 ILE H 46 " pdb=" CG2 ILE H 46 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB ILE H 26 " pdb=" CA ILE H 26 " pdb=" CG1 ILE H 26 " pdb=" CG2 ILE H 26 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1730 not shown) Planarity restraints: 1077 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 107 " 0.014 2.00e-02 2.50e+03 2.83e-02 8.00e+00 pdb=" C GLU C 107 " -0.049 2.00e-02 2.50e+03 pdb=" O GLU C 107 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP C 108 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 78 " 0.241 9.50e-02 1.11e+02 1.08e-01 7.15e+00 pdb=" NE ARG D 78 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG D 78 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG D 78 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 78 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 50 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.43e+00 pdb=" C ILE B 50 " -0.040 2.00e-02 2.50e+03 pdb=" O ILE B 50 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR B 51 " 0.014 2.00e-02 2.50e+03 ... (remaining 1074 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1756 2.78 - 3.31: 9056 3.31 - 3.84: 19758 3.84 - 4.37: 22053 4.37 - 4.90: 31413 Nonbonded interactions: 84036 Sorted by model distance: nonbonded pdb=" OE2 GLU B 63 " pdb=" NZ LYS F 91 " model vdw 2.253 3.120 nonbonded pdb=" OG SER C 68 " pdb=" NH2 ARG C 72 " model vdw 2.259 3.120 nonbonded pdb=" O LEU C 61 " pdb=" NH2 ARG D 36 " model vdw 2.291 3.120 nonbonded pdb=" NH2 ARG G 72 " pdb=" OP1 DC I 8 " model vdw 2.298 3.120 nonbonded pdb=" N VAL A 119 " pdb=" OP1 DC J 28 " model vdw 2.325 3.120 ... (remaining 84031 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and resid 59 through 134) selection = (chain 'E' and resid 59 through 134) selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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 group one per residue 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: 13.720 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 29.750 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10488 Z= 0.198 Angle : 0.655 7.280 15203 Z= 0.411 Chirality : 0.039 0.543 1733 Planarity : 0.006 0.108 1077 Dihedral : 28.694 164.584 4480 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 0.80 % Allowed : 4.41 % Favored : 94.79 % 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: 0.22 (0.29), residues: 583 helix: 0.48 (0.20), residues: 473 sheet: None (None), residues: 0 loop : -0.88 (0.43), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 86 HIS 0.002 0.001 HIS E 115 PHE 0.018 0.002 PHE E 106 TYR 0.018 0.002 TYR D 88 ARG 0.010 0.001 ARG E 130 Details of bonding type rmsd hydrogen bonds : bond 0.10569 ( 672) hydrogen bonds : angle 3.60412 ( 1674) covalent geometry : bond 0.00394 (10488) covalent geometry : angle 0.65478 (15203) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: E 78 PHE cc_start: 0.7743 (m-80) cc_final: 0.7333 (m-80) REVERT: E 85 ASN cc_start: 0.8309 (m-40) cc_final: 0.8053 (m-40) REVERT: G 80 ARG cc_start: 0.7452 (mtm-85) cc_final: 0.7070 (ptp90) REVERT: H 91 LYS cc_start: 0.7721 (tttt) cc_final: 0.7345 (mttt) REVERT: H 93 GLN cc_start: 0.7574 (tm-30) cc_final: 0.7269 (tm-30) outliers start: 4 outliers final: 0 residues processed: 83 average time/residue: 0.4748 time to fit residues: 46.6048 Evaluate side-chains 57 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 7.9990 chunk 60 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 0.1980 chunk 40 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 72 optimal weight: 6.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN C 85 ASN D 27 GLN E 115 HIS H 75 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.214387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.158490 restraints weight = 11759.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.155816 restraints weight = 23725.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.157662 restraints weight = 17940.600| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10488 Z= 0.155 Angle : 0.566 5.032 15203 Z= 0.337 Chirality : 0.034 0.135 1733 Planarity : 0.004 0.032 1077 Dihedral : 31.872 172.329 3289 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.80 % Allowed : 8.62 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.67 (0.33), residues: 583 helix: 2.52 (0.23), residues: 458 sheet: None (None), residues: 0 loop : -1.23 (0.38), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 86 HIS 0.001 0.001 HIS B 75 PHE 0.012 0.001 PHE E 67 TYR 0.013 0.002 TYR D 88 ARG 0.006 0.001 ARG H 40 Details of bonding type rmsd hydrogen bonds : bond 0.04365 ( 672) hydrogen bonds : angle 2.74829 ( 1674) covalent geometry : bond 0.00341 (10488) covalent geometry : angle 0.56554 (15203) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.720 Fit side-chains revert: symmetry clash REVERT: B 92 ARG cc_start: 0.7404 (ttp80) cc_final: 0.7123 (ttm-80) REVERT: D 50 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8024 (tp) REVERT: E 85 ASN cc_start: 0.8074 (m-40) cc_final: 0.7873 (m-40) REVERT: F 39 ARG cc_start: 0.8028 (mpt180) cc_final: 0.7751 (mmt180) REVERT: H 91 LYS cc_start: 0.8015 (tttt) cc_final: 0.7748 (ttmt) outliers start: 9 outliers final: 5 residues processed: 69 average time/residue: 0.3780 time to fit residues: 33.0984 Evaluate side-chains 59 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain H residue 82 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 9 optimal weight: 0.0370 chunk 19 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 64 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN ** G 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.205822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.145016 restraints weight = 11806.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.142071 restraints weight = 21075.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.144609 restraints weight = 15426.086| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10488 Z= 0.177 Angle : 0.574 6.301 15203 Z= 0.339 Chirality : 0.035 0.180 1733 Planarity : 0.004 0.034 1077 Dihedral : 32.093 172.973 3289 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 2.81 % Allowed : 9.62 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.87 (0.33), residues: 583 helix: 2.65 (0.23), residues: 458 sheet: None (None), residues: 0 loop : -1.11 (0.39), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 86 HIS 0.004 0.001 HIS H 75 PHE 0.010 0.001 PHE A 67 TYR 0.019 0.002 TYR F 88 ARG 0.004 0.000 ARG H 40 Details of bonding type rmsd hydrogen bonds : bond 0.04801 ( 672) hydrogen bonds : angle 2.80005 ( 1674) covalent geometry : bond 0.00403 (10488) covalent geometry : angle 0.57351 (15203) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.696 Fit side-chains REVERT: B 88 TYR cc_start: 0.9061 (m-80) cc_final: 0.8858 (m-80) REVERT: B 92 ARG cc_start: 0.7519 (ttp80) cc_final: 0.7018 (ttm170) REVERT: E 122 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.8341 (m-80) REVERT: H 93 GLN cc_start: 0.7851 (tm-30) cc_final: 0.7593 (tm-30) outliers start: 14 outliers final: 9 residues processed: 80 average time/residue: 0.3656 time to fit residues: 36.3523 Evaluate side-chains 64 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 82 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 9 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN E 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.198038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.138124 restraints weight = 11772.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.140484 restraints weight = 26008.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.141566 restraints weight = 18125.233| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10488 Z= 0.219 Angle : 0.621 7.789 15203 Z= 0.362 Chirality : 0.036 0.158 1733 Planarity : 0.005 0.062 1077 Dihedral : 32.490 178.919 3289 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.41 % Allowed : 12.22 % Favored : 84.37 % 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: 2.57 (0.33), residues: 583 helix: 2.43 (0.23), residues: 459 sheet: None (None), residues: 0 loop : -1.21 (0.42), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 86 HIS 0.005 0.001 HIS C 59 PHE 0.013 0.002 PHE A 78 TYR 0.024 0.002 TYR F 88 ARG 0.017 0.001 ARG D 39 Details of bonding type rmsd hydrogen bonds : bond 0.05177 ( 672) hydrogen bonds : angle 2.92371 ( 1674) covalent geometry : bond 0.00518 (10488) covalent geometry : angle 0.62090 (15203) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.654 Fit side-chains REVERT: C 72 ARG cc_start: 0.7963 (mtm-85) cc_final: 0.7529 (mtt180) REVERT: F 72 TYR cc_start: 0.7682 (m-10) cc_final: 0.7397 (m-80) REVERT: F 77 LYS cc_start: 0.7387 (mmmt) cc_final: 0.7137 (mmtp) REVERT: H 93 GLN cc_start: 0.8147 (tm-30) cc_final: 0.7903 (tm-30) outliers start: 17 outliers final: 9 residues processed: 76 average time/residue: 0.3367 time to fit residues: 32.4499 Evaluate side-chains 62 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 82 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 31 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 20 optimal weight: 0.3980 chunk 79 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.200249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.142309 restraints weight = 11774.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.141624 restraints weight = 23360.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.143524 restraints weight = 19192.459| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10488 Z= 0.154 Angle : 0.543 7.869 15203 Z= 0.325 Chirality : 0.033 0.125 1733 Planarity : 0.004 0.034 1077 Dihedral : 32.231 177.758 3289 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 2.61 % Allowed : 13.23 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.03 (0.33), residues: 583 helix: 2.77 (0.23), residues: 459 sheet: None (None), residues: 0 loop : -1.11 (0.42), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 86 HIS 0.001 0.000 HIS H 75 PHE 0.009 0.001 PHE E 67 TYR 0.013 0.001 TYR F 88 ARG 0.005 0.000 ARG B 39 Details of bonding type rmsd hydrogen bonds : bond 0.04190 ( 672) hydrogen bonds : angle 2.62153 ( 1674) covalent geometry : bond 0.00340 (10488) covalent geometry : angle 0.54326 (15203) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.686 Fit side-chains REVERT: B 92 ARG cc_start: 0.7539 (ttp80) cc_final: 0.7295 (ttm170) REVERT: E 122 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.8357 (m-80) REVERT: F 77 LYS cc_start: 0.7274 (mmmt) cc_final: 0.7032 (mmtp) REVERT: H 93 GLN cc_start: 0.8074 (tm-30) cc_final: 0.7806 (tm-30) outliers start: 13 outliers final: 7 residues processed: 68 average time/residue: 0.3113 time to fit residues: 27.4600 Evaluate side-chains 60 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain D residue 72 TYR Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 82 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 22 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 45 optimal weight: 0.0030 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.199854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.144660 restraints weight = 11851.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.142144 restraints weight = 22882.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.143804 restraints weight = 17641.749| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10488 Z= 0.159 Angle : 0.546 6.935 15203 Z= 0.325 Chirality : 0.033 0.137 1733 Planarity : 0.004 0.032 1077 Dihedral : 32.242 178.559 3289 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.40 % Allowed : 14.43 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.13 (0.33), residues: 583 helix: 2.84 (0.23), residues: 459 sheet: None (None), residues: 0 loop : -1.07 (0.42), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 86 HIS 0.002 0.000 HIS H 75 PHE 0.009 0.001 PHE A 67 TYR 0.013 0.002 TYR F 88 ARG 0.005 0.000 ARG D 35 Details of bonding type rmsd hydrogen bonds : bond 0.04339 ( 672) hydrogen bonds : angle 2.60127 ( 1674) covalent geometry : bond 0.00356 (10488) covalent geometry : angle 0.54639 (15203) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.677 Fit side-chains REVERT: B 92 ARG cc_start: 0.7563 (ttp80) cc_final: 0.7211 (ttm170) REVERT: D 44 LYS cc_start: 0.5881 (mtpp) cc_final: 0.5299 (mmmt) REVERT: F 77 LYS cc_start: 0.7217 (mmmt) cc_final: 0.7003 (mmtp) outliers start: 12 outliers final: 7 residues processed: 67 average time/residue: 0.3414 time to fit residues: 28.9832 Evaluate side-chains 62 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 82 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 53 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 79 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.201279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.147050 restraints weight = 11970.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.145809 restraints weight = 25758.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.147424 restraints weight = 21892.828| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10488 Z= 0.153 Angle : 0.536 6.620 15203 Z= 0.319 Chirality : 0.032 0.128 1733 Planarity : 0.003 0.032 1077 Dihedral : 32.114 178.587 3289 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.61 % Allowed : 13.23 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.21 (0.33), residues: 583 helix: 2.90 (0.23), residues: 459 sheet: None (None), residues: 0 loop : -1.09 (0.42), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 86 HIS 0.002 0.000 HIS H 75 PHE 0.007 0.001 PHE E 67 TYR 0.013 0.001 TYR F 88 ARG 0.004 0.000 ARG D 92 Details of bonding type rmsd hydrogen bonds : bond 0.04169 ( 672) hydrogen bonds : angle 2.53687 ( 1674) covalent geometry : bond 0.00340 (10488) covalent geometry : angle 0.53562 (15203) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.653 Fit side-chains REVERT: D 44 LYS cc_start: 0.5902 (mtpp) cc_final: 0.5280 (mmmt) REVERT: E 122 PHE cc_start: 0.8591 (OUTLIER) cc_final: 0.8283 (m-80) REVERT: H 93 GLN cc_start: 0.7912 (tm-30) cc_final: 0.7627 (tm-30) outliers start: 13 outliers final: 9 residues processed: 65 average time/residue: 0.2940 time to fit residues: 25.1526 Evaluate side-chains 63 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 82 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 10 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.191409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.137793 restraints weight = 11936.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.135698 restraints weight = 28155.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.137856 restraints weight = 20472.546| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 10488 Z= 0.239 Angle : 0.634 7.771 15203 Z= 0.367 Chirality : 0.037 0.149 1733 Planarity : 0.004 0.032 1077 Dihedral : 32.574 177.427 3289 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.01 % Allowed : 13.83 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.56 (0.33), residues: 583 helix: 2.41 (0.23), residues: 459 sheet: None (None), residues: 0 loop : -1.15 (0.43), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 86 HIS 0.003 0.001 HIS A 115 PHE 0.015 0.002 PHE A 67 TYR 0.027 0.003 TYR F 88 ARG 0.008 0.001 ARG H 40 Details of bonding type rmsd hydrogen bonds : bond 0.05417 ( 672) hydrogen bonds : angle 2.88791 ( 1674) covalent geometry : bond 0.00570 (10488) covalent geometry : angle 0.63426 (15203) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.865 Fit side-chains REVERT: D 44 LYS cc_start: 0.5954 (mtpp) cc_final: 0.5451 (mmmt) REVERT: E 122 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.8575 (m-80) outliers start: 15 outliers final: 11 residues processed: 70 average time/residue: 0.3568 time to fit residues: 32.9704 Evaluate side-chains 66 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 82 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 14 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 75 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.197554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.145598 restraints weight = 11762.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.142892 restraints weight = 25629.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.144481 restraints weight = 19447.469| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.5310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10488 Z= 0.153 Angle : 0.549 7.385 15203 Z= 0.326 Chirality : 0.033 0.121 1733 Planarity : 0.003 0.034 1077 Dihedral : 32.267 179.720 3289 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.00 % Allowed : 15.43 % Favored : 82.57 % 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: 3.01 (0.33), residues: 583 helix: 2.76 (0.23), residues: 459 sheet: None (None), residues: 0 loop : -1.18 (0.43), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 86 HIS 0.002 0.001 HIS G 115 PHE 0.011 0.001 PHE E 78 TYR 0.014 0.001 TYR D 88 ARG 0.005 0.000 ARG H 40 Details of bonding type rmsd hydrogen bonds : bond 0.04209 ( 672) hydrogen bonds : angle 2.58086 ( 1674) covalent geometry : bond 0.00338 (10488) covalent geometry : angle 0.54914 (15203) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.664 Fit side-chains REVERT: D 44 LYS cc_start: 0.5711 (mtpp) cc_final: 0.5030 (mmmt) REVERT: E 122 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.8381 (m-80) REVERT: H 93 GLN cc_start: 0.7768 (tm-30) cc_final: 0.7521 (tm-30) outliers start: 10 outliers final: 7 residues processed: 60 average time/residue: 0.2754 time to fit residues: 22.0817 Evaluate side-chains 58 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 82 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 58 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.194904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.139422 restraints weight = 11743.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.141136 restraints weight = 26114.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.141172 restraints weight = 14405.918| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.5538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10488 Z= 0.186 Angle : 0.584 7.326 15203 Z= 0.341 Chirality : 0.034 0.136 1733 Planarity : 0.004 0.032 1077 Dihedral : 32.371 178.526 3289 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.80 % Allowed : 15.43 % Favored : 82.77 % 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: 2.89 (0.33), residues: 583 helix: 2.67 (0.23), residues: 459 sheet: None (None), residues: 0 loop : -1.18 (0.43), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 86 HIS 0.002 0.001 HIS A 115 PHE 0.011 0.001 PHE A 67 TYR 0.017 0.002 TYR D 88 ARG 0.005 0.001 ARG H 40 Details of bonding type rmsd hydrogen bonds : bond 0.04740 ( 672) hydrogen bonds : angle 2.69900 ( 1674) covalent geometry : bond 0.00433 (10488) covalent geometry : angle 0.58361 (15203) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.820 Fit side-chains REVERT: D 44 LYS cc_start: 0.5802 (mtpp) cc_final: 0.5237 (mmmt) REVERT: D 50 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8135 (tp) REVERT: E 122 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.8435 (m-80) outliers start: 9 outliers final: 7 residues processed: 62 average time/residue: 0.3478 time to fit residues: 27.9296 Evaluate side-chains 62 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 82 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 65 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 73 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.195832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.139019 restraints weight = 11726.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.139295 restraints weight = 26655.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.140794 restraints weight = 19221.966| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.5734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10488 Z= 0.171 Angle : 0.561 7.958 15203 Z= 0.331 Chirality : 0.033 0.133 1733 Planarity : 0.004 0.033 1077 Dihedral : 32.268 178.890 3289 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.00 % Allowed : 15.83 % Favored : 82.16 % 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: 2.99 (0.33), residues: 583 helix: 2.75 (0.23), residues: 459 sheet: None (None), residues: 0 loop : -1.19 (0.43), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 86 HIS 0.002 0.001 HIS H 75 PHE 0.011 0.001 PHE E 78 TYR 0.013 0.001 TYR D 88 ARG 0.005 0.000 ARG H 40 Details of bonding type rmsd hydrogen bonds : bond 0.04458 ( 672) hydrogen bonds : angle 2.61646 ( 1674) covalent geometry : bond 0.00389 (10488) covalent geometry : angle 0.56060 (15203) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2799.07 seconds wall clock time: 50 minutes 39.86 seconds (3039.86 seconds total)