Starting phenix.real_space_refine on Mon May 12 22:55:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k9l_62193/05_2025/9k9l_62193.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k9l_62193/05_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_62193/05_2025/9k9l_62193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k9l_62193/05_2025/9k9l_62193.map" model { file = "/net/cci-nas-00/data/ceres_data/9k9l_62193/05_2025/9k9l_62193.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k9l_62193/05_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-5687/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: 6.03, per 1000 atoms: 0.61 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: 2.58 Conformation dependent library (CDL) restraints added in 605.9 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: 4.67 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: 3.50 Time building geometry restraints manager: 3.03 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: 0.650 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.140 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.350 ------------------------------------------------------------------------------- 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 : 0.639 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: 0.4754 time to fit residues: 46.6697 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 : 0.646 ------------------------------------------------------------------------------- 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 = 0.4379 r_free = 0.4379 target = 0.215118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.151315 restraints weight = 11754.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.149763 restraints weight = 17261.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.151187 restraints weight = 15153.415| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 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 : 0.694 Fit side-chains revert: symmetry clash REVERT: B 92 ARG cc_start: 0.7388 (ttp80) cc_final: 0.7098 (ttm-80) REVERT: D 50 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.7971 (tp) REVERT: E 85 ASN cc_start: 0.8141 (m-40) cc_final: 0.7858 (m-40) REVERT: F 39 ARG cc_start: 0.8077 (mpt180) cc_final: 0.7788 (mmt180) REVERT: H 91 LYS cc_start: 0.7901 (tttt) cc_final: 0.7614 (ttmt) outliers start: 9 outliers final: 5 residues processed: 69 average time/residue: 0.3372 time to fit residues: 29.5174 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 : 0.698 ------------------------------------------------------------------------------- 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: 2.9990 chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- 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 = 0.4293 r_free = 0.4293 target = 0.206287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.144344 restraints weight = 11794.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.145151 restraints weight = 23018.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.146516 restraints weight = 21209.520| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10488 Z= 0.170 Angle : 0.560 5.592 15203 Z= 0.332 Chirality : 0.034 0.174 1733 Planarity : 0.003 0.032 1077 Dihedral : 32.021 172.347 3289 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 2.61 % Allowed : 10.42 % Favored : 86.97 % 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: 3.02 (0.33), residues: 583 helix: 2.74 (0.23), residues: 458 sheet: None (None), residues: 0 loop : -1.01 (0.40), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 86 HIS 0.004 0.001 HIS H 75 PHE 0.009 0.001 PHE A 67 TYR 0.018 0.002 TYR F 88 ARG 0.004 0.000 ARG H 40 Details of bonding type rmsd hydrogen bonds : bond 0.04662 ( 672) hydrogen bonds : angle 2.74775 ( 1674) covalent geometry : bond 0.00383 (10488) covalent geometry : angle 0.56020 (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 79 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.643 Fit side-chains REVERT: D 50 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8136 (tp) outliers start: 13 outliers final: 9 residues processed: 78 average time/residue: 0.3410 time to fit residues: 33.1797 Evaluate side-chains 61 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 D residue 50 ILE 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: 0.9980 chunk 46 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 53 optimal weight: 0.5980 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: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4315 r_free = 0.4315 target = 0.208674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.147574 restraints weight = 11703.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.145491 restraints weight = 18614.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.147114 restraints weight = 14883.572| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.3037 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= 0.157 Angle : 0.540 5.802 15203 Z= 0.323 Chirality : 0.033 0.130 1733 Planarity : 0.004 0.032 1077 Dihedral : 31.980 174.126 3289 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 3.41 % Allowed : 11.82 % Favored : 84.77 % 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: 3.26 (0.33), residues: 583 helix: 2.89 (0.23), residues: 458 sheet: None (None), residues: 0 loop : -0.82 (0.43), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 86 HIS 0.004 0.001 HIS C 59 PHE 0.009 0.001 PHE E 67 TYR 0.016 0.001 TYR D 88 ARG 0.005 0.000 ARG H 40 Details of bonding type rmsd hydrogen bonds : bond 0.04216 ( 672) hydrogen bonds : angle 2.60243 ( 1674) covalent geometry : bond 0.00347 (10488) covalent geometry : angle 0.54045 (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 78 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.702 Fit side-chains REVERT: B 92 ARG cc_start: 0.7345 (ttp80) cc_final: 0.6852 (ttm-80) REVERT: E 122 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.8280 (m-80) REVERT: F 72 TYR cc_start: 0.7634 (m-10) cc_final: 0.7258 (m-80) REVERT: F 77 LYS cc_start: 0.7094 (mmmt) cc_final: 0.6879 (mmtp) outliers start: 17 outliers final: 8 residues processed: 74 average time/residue: 0.3116 time to fit residues: 29.6339 Evaluate side-chains 63 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain F residue 25 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 31 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 34 optimal weight: 0.3980 chunk 45 optimal weight: 0.5980 chunk 21 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 6 optimal weight: 0.0050 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 = 0.4352 r_free = 0.4352 target = 0.212719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.151889 restraints weight = 11641.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.153134 restraints weight = 20635.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.154219 restraints weight = 20217.949| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3401 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= 0.148 Angle : 0.533 8.231 15203 Z= 0.318 Chirality : 0.032 0.127 1733 Planarity : 0.003 0.031 1077 Dihedral : 31.918 174.425 3289 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.40 % Allowed : 12.42 % Favored : 85.17 % 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: 3.39 (0.33), residues: 583 helix: 2.99 (0.23), residues: 459 sheet: None (None), residues: 0 loop : -0.85 (0.43), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 86 HIS 0.002 0.000 HIS H 75 PHE 0.007 0.001 PHE E 78 TYR 0.014 0.001 TYR F 88 ARG 0.006 0.000 ARG D 78 Details of bonding type rmsd hydrogen bonds : bond 0.04107 ( 672) hydrogen bonds : angle 2.54021 ( 1674) covalent geometry : bond 0.00324 (10488) covalent geometry : angle 0.53256 (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 70 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.654 Fit side-chains REVERT: B 92 ARG cc_start: 0.7624 (ttp80) cc_final: 0.7297 (ttm-80) REVERT: D 50 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8156 (tp) REVERT: E 122 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.8245 (m-80) REVERT: F 77 LYS cc_start: 0.7055 (mmmt) cc_final: 0.6806 (mmtp) outliers start: 12 outliers final: 6 residues processed: 68 average time/residue: 0.3351 time to fit residues: 29.1150 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 : 0.664 ------------------------------------------------------------------------------- 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 50 ILE Chi-restraints excluded: chain E residue 122 PHE 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: 0.7980 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4277 r_free = 0.4277 target = 0.205317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.145727 restraints weight = 11871.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.146906 restraints weight = 26542.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.148467 restraints weight = 19541.506| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.3826 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= 0.152 Angle : 0.533 7.355 15203 Z= 0.318 Chirality : 0.033 0.127 1733 Planarity : 0.003 0.031 1077 Dihedral : 31.910 175.447 3289 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.61 % Allowed : 11.82 % Favored : 85.57 % 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: 3.45 (0.33), residues: 583 helix: 3.03 (0.23), residues: 459 sheet: None (None), residues: 0 loop : -0.82 (0.44), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 86 HIS 0.001 0.000 HIS H 75 PHE 0.007 0.001 PHE A 67 TYR 0.013 0.002 TYR F 88 ARG 0.007 0.000 ARG B 39 Details of bonding type rmsd hydrogen bonds : bond 0.04181 ( 672) hydrogen bonds : angle 2.52342 ( 1674) covalent geometry : bond 0.00335 (10488) covalent geometry : angle 0.53262 (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: 13 poor density : 56 time to evaluate : 0.725 Fit side-chains REVERT: B 92 ARG cc_start: 0.7635 (ttp80) cc_final: 0.7317 (ttm-80) outliers start: 13 outliers final: 10 residues processed: 66 average time/residue: 0.3395 time to fit residues: 28.5668 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 : 0.634 ------------------------------------------------------------------------------- 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 70 VAL Chi-restraints excluded: chain D residue 72 TYR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 73 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 53 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 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: 0.7980 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 27 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN G 115 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.204119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.145103 restraints weight = 11945.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.143646 restraints weight = 23394.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.145679 restraints weight = 19589.302| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.4176 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 : 0.533 6.525 15203 Z= 0.318 Chirality : 0.033 0.140 1733 Planarity : 0.003 0.031 1077 Dihedral : 31.923 176.519 3289 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.61 % Allowed : 12.63 % Favored : 84.77 % 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: 3.43 (0.33), residues: 583 helix: 3.02 (0.23), residues: 459 sheet: None (None), residues: 0 loop : -0.84 (0.44), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 86 HIS 0.002 0.001 HIS A 115 PHE 0.008 0.001 PHE E 122 TYR 0.013 0.001 TYR F 88 ARG 0.006 0.000 ARG H 40 Details of bonding type rmsd hydrogen bonds : bond 0.04194 ( 672) hydrogen bonds : angle 2.54095 ( 1674) covalent geometry : bond 0.00341 (10488) covalent geometry : angle 0.53320 (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 67 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.658 Fit side-chains REVERT: B 92 ARG cc_start: 0.7666 (ttp80) cc_final: 0.7317 (ttm-80) REVERT: D 44 LYS cc_start: 0.5794 (mtpp) cc_final: 0.5224 (mmmt) REVERT: D 50 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.8041 (tp) outliers start: 13 outliers final: 10 residues processed: 66 average time/residue: 0.2895 time to fit residues: 24.8838 Evaluate side-chains 63 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 50 ILE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 73 THR 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: 1.9990 chunk 73 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.4176 r_free = 0.4176 target = 0.195190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.137538 restraints weight = 12008.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.137676 restraints weight = 30062.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.139315 restraints weight = 22953.458| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10488 Z= 0.213 Angle : 0.608 9.028 15203 Z= 0.353 Chirality : 0.035 0.180 1733 Planarity : 0.004 0.033 1077 Dihedral : 32.324 179.410 3289 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.40 % Allowed : 13.63 % Favored : 83.97 % 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: 2.91 (0.33), residues: 583 helix: 2.64 (0.23), residues: 459 sheet: None (None), residues: 0 loop : -0.92 (0.44), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 86 HIS 0.003 0.001 HIS A 115 PHE 0.015 0.002 PHE A 67 TYR 0.025 0.002 TYR F 88 ARG 0.007 0.001 ARG H 40 Details of bonding type rmsd hydrogen bonds : bond 0.05065 ( 672) hydrogen bonds : angle 2.81470 ( 1674) covalent geometry : bond 0.00501 (10488) covalent geometry : angle 0.60768 (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 65 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.780 Fit side-chains REVERT: D 44 LYS cc_start: 0.5933 (mtpp) cc_final: 0.5254 (mmmt) outliers start: 12 outliers final: 9 residues processed: 64 average time/residue: 0.3156 time to fit residues: 26.1835 Evaluate side-chains 59 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 D residue 70 VAL 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 14 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.4202 r_free = 0.4202 target = 0.198018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.144571 restraints weight = 11850.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.142080 restraints weight = 25200.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.143610 restraints weight = 19913.606| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10488 Z= 0.165 Angle : 0.551 6.665 15203 Z= 0.327 Chirality : 0.033 0.134 1733 Planarity : 0.004 0.032 1077 Dihedral : 32.170 179.853 3289 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.60 % Allowed : 14.23 % 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: 3.13 (0.33), residues: 583 helix: 2.81 (0.23), residues: 459 sheet: None (None), residues: 0 loop : -0.96 (0.44), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 86 HIS 0.002 0.001 HIS H 75 PHE 0.008 0.001 PHE E 67 TYR 0.013 0.001 TYR F 88 ARG 0.007 0.000 ARG H 40 Details of bonding type rmsd hydrogen bonds : bond 0.04361 ( 672) hydrogen bonds : angle 2.61952 ( 1674) covalent geometry : bond 0.00373 (10488) covalent geometry : angle 0.55076 (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 58 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.730 Fit side-chains REVERT: D 44 LYS cc_start: 0.5837 (mtpp) cc_final: 0.5245 (mmmt) outliers start: 8 outliers final: 8 residues processed: 57 average time/residue: 0.2969 time to fit residues: 22.3958 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 : 0.682 ------------------------------------------------------------------------------- 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 70 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 14 optimal weight: 0.0060 chunk 44 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 0.1980 chunk 58 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.197243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.141422 restraints weight = 11812.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.143698 restraints weight = 28806.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.144671 restraints weight = 19278.965| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.5304 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= 0.169 Angle : 0.554 7.124 15203 Z= 0.329 Chirality : 0.033 0.153 1733 Planarity : 0.004 0.033 1077 Dihedral : 32.161 179.768 3289 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.20 % Allowed : 14.23 % Favored : 83.57 % 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: 3.18 (0.33), residues: 583 helix: 2.87 (0.23), residues: 459 sheet: None (None), residues: 0 loop : -1.03 (0.44), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 86 HIS 0.002 0.001 HIS H 75 PHE 0.009 0.001 PHE A 67 TYR 0.015 0.001 TYR F 88 ARG 0.005 0.000 ARG H 40 Details of bonding type rmsd hydrogen bonds : bond 0.04506 ( 672) hydrogen bonds : angle 2.61680 ( 1674) covalent geometry : bond 0.00385 (10488) covalent geometry : angle 0.55394 (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 63 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.716 Fit side-chains REVERT: D 44 LYS cc_start: 0.5814 (mtpp) cc_final: 0.5324 (mmmt) REVERT: F 72 TYR cc_start: 0.7371 (m-80) cc_final: 0.7066 (m-80) REVERT: H 93 GLN cc_start: 0.8242 (tm-30) cc_final: 0.8020 (tm-30) outliers start: 11 outliers final: 10 residues processed: 62 average time/residue: 0.2979 time to fit residues: 24.1960 Evaluate side-chains 61 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 D residue 70 VAL 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=1.00 ------------------------------------------------------------------------------- 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: 0.9980 chunk 73 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.4150 r_free = 0.4150 target = 0.193239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.134234 restraints weight = 11746.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.132490 restraints weight = 23457.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.134211 restraints weight = 19438.947| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.5657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10488 Z= 0.201 Angle : 0.591 7.335 15203 Z= 0.347 Chirality : 0.035 0.158 1733 Planarity : 0.004 0.032 1077 Dihedral : 32.364 177.893 3289 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.81 % Allowed : 14.23 % Favored : 82.97 % 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: 2.88 (0.33), residues: 583 helix: 2.65 (0.23), residues: 459 sheet: None (None), residues: 0 loop : -1.12 (0.45), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 86 HIS 0.002 0.001 HIS A 115 PHE 0.012 0.001 PHE A 67 TYR 0.019 0.002 TYR F 88 ARG 0.010 0.001 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.04923 ( 672) hydrogen bonds : angle 2.76302 ( 1674) covalent geometry : bond 0.00472 (10488) covalent geometry : angle 0.59144 (15203) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2509.00 seconds wall clock time: 44 minutes 41.40 seconds (2681.40 seconds total)