Starting phenix.real_space_refine on Tue Apr 29 00:30:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ooa_17008/04_2025/8ooa_17008.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ooa_17008/04_2025/8ooa_17008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ooa_17008/04_2025/8ooa_17008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ooa_17008/04_2025/8ooa_17008.map" model { file = "/net/cci-nas-00/data/ceres_data/8ooa_17008/04_2025/8ooa_17008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ooa_17008/04_2025/8ooa_17008.cif" } resolution = 3.18 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= 0.001 sd= 0.022 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 204 5.49 5 S 12 5.16 5 C 4638 2.51 5 N 1589 2.21 5 O 1962 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8405 Number of models: 1 Model: "" Number of chains: 8 Chain: "K" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 2086 Classifications: {'DNA': 102} Link IDs: {'rna3p': 101} Chain: "L" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 2096 Classifications: {'DNA': 102} Link IDs: {'rna3p': 101} Chain: "M" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 602 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "N" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 602 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "O" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "P" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 729 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "Q" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "R" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Time building chain proxies: 6.03, per 1000 atoms: 0.72 Number of scatterers: 8405 At special positions: 0 Unit cell: (114.258, 115.902, 77.268, 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 12 16.00 P 204 15.00 O 1962 8.00 N 1589 7.00 C 4638 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: 2.25 Conformation dependent library (CDL) restraints added in 532.6 milliseconds 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 990 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 7 sheets defined 74.3% alpha, 3.0% beta 58 base pairs and 190 stacking pairs defined. Time for finding SS restraints: 3.92 Creating SS restraints... Processing helix chain 'M' and resid 63 through 77 removed outlier: 4.267A pdb=" N ASP M 77 " --> pdb=" O GLU M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 113 removed outlier: 3.905A pdb=" N ASP M 106 " --> pdb=" O GLY M 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 114 through 116 No H-bonds generated for 'chain 'M' and resid 114 through 116' Processing helix chain 'M' and resid 120 through 131 Processing helix chain 'N' and resid 24 through 29 removed outlier: 3.645A pdb=" N ILE N 29 " --> pdb=" O ILE N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 41 Processing helix chain 'N' and resid 47 through 76 removed outlier: 4.178A pdb=" N TYR N 51 " --> pdb=" O SER N 47 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU N 52 " --> pdb=" O GLY N 48 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN N 64 " --> pdb=" O VAL N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 95 Processing helix chain 'O' and resid 16 through 22 Processing helix chain 'O' and resid 26 through 37 Processing helix chain 'O' and resid 46 through 73 Processing helix chain 'O' and resid 79 through 89 Processing helix chain 'O' and resid 92 through 97 Processing helix chain 'O' and resid 112 through 116 Processing helix chain 'P' and resid 34 through 43 Processing helix chain 'P' and resid 52 through 81 Processing helix chain 'P' and resid 87 through 99 Processing helix chain 'P' and resid 100 through 122 Processing helix chain 'Q' and resid 44 through 55 Processing helix chain 'Q' and resid 63 through 77 removed outlier: 4.209A pdb=" N ASP Q 77 " --> pdb=" O GLU Q 73 " (cutoff:3.500A) Processing helix chain 'Q' and resid 85 through 114 removed outlier: 3.507A pdb=" N ASP Q 106 " --> pdb=" O GLY Q 102 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 131 removed outlier: 3.529A pdb=" N ILE Q 124 " --> pdb=" O MET Q 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 29 Processing helix chain 'R' and resid 30 through 41 Processing helix chain 'R' and resid 49 through 76 removed outlier: 3.639A pdb=" N GLU R 53 " --> pdb=" O LEU R 49 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN R 64 " --> pdb=" O VAL R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 93 Processing sheet with id=AA1, first strand: chain 'M' and resid 83 through 84 removed outlier: 6.671A pdb=" N ARG M 83 " --> pdb=" O VAL N 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'M' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'O' and resid 42 through 43 removed outlier: 7.220A pdb=" N ARG O 42 " --> pdb=" O ILE P 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'O' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'O' and resid 100 through 102 removed outlier: 6.523A pdb=" N THR O 101 " --> pdb=" O TYR R 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'Q' and resid 83 through 84 removed outlier: 6.382A pdb=" N ARG Q 83 " --> pdb=" O VAL R 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'Q' and resid 118 through 119 284 hydrogen bonds defined for protein. 831 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 141 hydrogen bonds 282 hydrogen bond angles 0 basepair planarities 58 basepair parallelities 190 stacking parallelities Total time for adding SS restraints: 2.93 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1955 1.34 - 1.45: 2579 1.45 - 1.57: 4002 1.57 - 1.69: 409 1.69 - 1.81: 20 Bond restraints: 8965 Sorted by residual: bond pdb=" C4' DG L 63 " pdb=" C3' DG L 63 " ideal model delta sigma weight residual 1.523 1.577 -0.054 2.00e-02 2.50e+03 7.17e+00 bond pdb=" C4' DG K 25 " pdb=" C3' DG K 25 " ideal model delta sigma weight residual 1.523 1.575 -0.052 2.00e-02 2.50e+03 6.80e+00 bond pdb=" C4' DG K 20 " pdb=" C3' DG K 20 " ideal model delta sigma weight residual 1.523 1.571 -0.048 2.00e-02 2.50e+03 5.77e+00 bond pdb=" C4' DG L -5 " pdb=" C3' DG L -5 " ideal model delta sigma weight residual 1.523 1.571 -0.048 2.00e-02 2.50e+03 5.75e+00 bond pdb=" C4' DC K 4 " pdb=" C3' DC K 4 " ideal model delta sigma weight residual 1.523 1.570 -0.047 2.00e-02 2.50e+03 5.42e+00 ... (remaining 8960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.95: 9801 0.95 - 1.90: 1946 1.90 - 2.85: 705 2.85 - 3.80: 470 3.80 - 4.75: 49 Bond angle restraints: 12971 Sorted by residual: angle pdb=" O3' DC L -25 " pdb=" P DT L -24 " pdb=" O5' DT L -24 " ideal model delta sigma weight residual 104.00 99.62 4.38 1.50e+00 4.44e-01 8.54e+00 angle pdb=" C4' DC K 21 " pdb=" O4' DC K 21 " pdb=" C1' DC K 21 " ideal model delta sigma weight residual 109.70 105.34 4.36 1.50e+00 4.44e-01 8.45e+00 angle pdb=" O3' DG L 27 " pdb=" P DA L 28 " pdb=" O5' DA L 28 " ideal model delta sigma weight residual 104.00 99.89 4.11 1.50e+00 4.44e-01 7.51e+00 angle pdb=" O3' DC L -28 " pdb=" P DC L -27 " pdb=" O5' DC L -27 " ideal model delta sigma weight residual 104.00 99.93 4.07 1.50e+00 4.44e-01 7.35e+00 angle pdb=" O3' DA K -45 " pdb=" P DA K -44 " pdb=" O5' DA K -44 " ideal model delta sigma weight residual 104.00 100.01 3.99 1.50e+00 4.44e-01 7.09e+00 ... (remaining 12966 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 3198 17.66 - 35.31: 630 35.31 - 52.97: 794 52.97 - 70.62: 212 70.62 - 88.28: 25 Dihedral angle restraints: 4859 sinusoidal: 3327 harmonic: 1532 Sorted by residual: dihedral pdb=" CA ILE M 112 " pdb=" C ILE M 112 " pdb=" N HIS M 113 " pdb=" CA HIS M 113 " ideal model delta harmonic sigma weight residual 180.00 152.41 27.59 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA ASP Q 81 " pdb=" C ASP Q 81 " pdb=" N LEU Q 82 " pdb=" CA LEU Q 82 " ideal model delta harmonic sigma weight residual 180.00 159.18 20.82 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA GLY N 28 " pdb=" C GLY N 28 " pdb=" N ILE N 29 " pdb=" CA ILE N 29 " ideal model delta harmonic sigma weight residual 180.00 159.35 20.65 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 4856 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 741 0.039 - 0.079: 516 0.079 - 0.118: 156 0.118 - 0.157: 51 0.157 - 0.196: 11 Chirality restraints: 1475 Sorted by residual: chirality pdb=" CB ILE N 29 " pdb=" CA ILE N 29 " pdb=" CG1 ILE N 29 " pdb=" CG2 ILE N 29 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.63e-01 chirality pdb=" C1' DT L 15 " pdb=" O4' DT L 15 " pdb=" C2' DT L 15 " pdb=" N1 DT L 15 " both_signs ideal model delta sigma weight residual False 2.47 2.28 0.19 2.00e-01 2.50e+01 9.05e-01 chirality pdb=" CA ILE O 79 " pdb=" N ILE O 79 " pdb=" C ILE O 79 " pdb=" CB ILE O 79 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.88e-01 ... (remaining 1472 not shown) Planarity restraints: 936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG N 92 " -0.324 9.50e-02 1.11e+02 1.46e-01 1.58e+01 pdb=" NE ARG N 92 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG N 92 " -0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG N 92 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG N 92 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 41 " 0.003 2.00e-02 2.50e+03 2.40e-02 1.15e+01 pdb=" CG TYR Q 41 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 41 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 41 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 41 " -0.034 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 41 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR Q 41 " -0.034 2.00e-02 2.50e+03 pdb=" OH TYR Q 41 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG M 83 " -0.240 9.50e-02 1.11e+02 1.08e-01 8.70e+00 pdb=" NE ARG M 83 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG M 83 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG M 83 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG M 83 " -0.001 2.00e-02 2.50e+03 ... (remaining 933 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1742 2.82 - 3.34: 7553 3.34 - 3.86: 16370 3.86 - 4.38: 20627 4.38 - 4.90: 28006 Nonbonded interactions: 74298 Sorted by model distance: nonbonded pdb=" OH TYR Q 99 " pdb=" OE1 GLU Q 133 " model vdw 2.299 3.040 nonbonded pdb=" OD2 ASP M 106 " pdb=" NH1 ARG M 131 " model vdw 2.377 3.120 nonbonded pdb=" OP1 DG L 8 " pdb=" N ILE N 46 " model vdw 2.398 3.120 nonbonded pdb=" OP1 DA L 28 " pdb=" N LYS N 79 " model vdw 2.412 3.120 nonbonded pdb=" OD2 ASP P 65 " pdb=" OH TYR R 98 " model vdw 2.425 3.040 ... (remaining 74293 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 'N' and resid 23 through 95) selection = (chain 'R' and resid 23 through 95) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.870 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: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.050 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 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 : 0.008 0.057 8965 Z= 0.378 Angle : 1.083 4.754 12971 Z= 0.589 Chirality : 0.057 0.196 1475 Planarity : 0.012 0.146 936 Dihedral : 27.962 88.276 3869 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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: -2.10 (0.30), residues: 517 helix: -1.41 (0.21), residues: 388 sheet: None (None), residues: 0 loop : -0.64 (0.46), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 75 PHE 0.026 0.002 PHE R 100 TYR 0.035 0.006 TYR Q 41 ARG 0.029 0.004 ARG N 92 Details of bonding type rmsd hydrogen bonds : bond 0.22375 ( 425) hydrogen bonds : angle 8.43492 ( 1113) covalent geometry : bond 0.00812 ( 8965) covalent geometry : angle 1.08321 (12971) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: N 57 VAL cc_start: 0.8072 (t) cc_final: 0.7789 (m) REVERT: N 91 LYS cc_start: 0.8304 (mttt) cc_final: 0.7853 (mtpt) REVERT: O 74 LYS cc_start: 0.7891 (mttt) cc_final: 0.7667 (mptt) REVERT: P 32 GLU cc_start: 0.6035 (mt-10) cc_final: 0.5638 (pt0) REVERT: P 44 GLN cc_start: 0.7192 (mt0) cc_final: 0.6991 (mt0) REVERT: Q 58 THR cc_start: 0.7089 (p) cc_final: 0.6852 (p) REVERT: Q 64 LYS cc_start: 0.7827 (mttt) cc_final: 0.7426 (mtpt) REVERT: Q 68 GLN cc_start: 0.8021 (mt0) cc_final: 0.7814 (mt0) REVERT: R 25 ASN cc_start: 0.7507 (m-40) cc_final: 0.7123 (m110) REVERT: R 57 VAL cc_start: 0.8440 (t) cc_final: 0.8096 (m) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.4160 time to fit residues: 61.0754 Evaluate side-chains 89 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.9990 chunk 53 optimal weight: 0.0010 chunk 29 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 125 GLN O 104 GLN P 60 ASN P 64 ASN P 79 HIS P 81 ASN R 75 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.127910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.110339 restraints weight = 11047.234| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 0.71 r_work: 0.3354 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8965 Z= 0.182 Angle : 0.590 4.828 12971 Z= 0.357 Chirality : 0.036 0.134 1475 Planarity : 0.004 0.032 936 Dihedral : 32.273 90.757 2801 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.68 % Allowed : 6.55 % Favored : 92.78 % 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: 1.20 (0.35), residues: 517 helix: 1.20 (0.25), residues: 384 sheet: None (None), residues: 0 loop : -0.19 (0.47), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS R 75 PHE 0.016 0.002 PHE P 62 TYR 0.019 0.002 TYR N 88 ARG 0.006 0.000 ARG P 76 Details of bonding type rmsd hydrogen bonds : bond 0.04869 ( 425) hydrogen bonds : angle 3.50170 ( 1113) covalent geometry : bond 0.00391 ( 8965) covalent geometry : angle 0.59021 (12971) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 96 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: N 91 LYS cc_start: 0.8060 (mttt) cc_final: 0.7551 (mmtt) REVERT: N 92 ARG cc_start: 0.7115 (mtp85) cc_final: 0.6875 (mtp85) REVERT: P 68 GLU cc_start: 0.6938 (mt-10) cc_final: 0.6679 (mt-10) REVERT: P 82 LYS cc_start: 0.7742 (mtmm) cc_final: 0.7342 (mttp) REVERT: Q 58 THR cc_start: 0.7186 (p) cc_final: 0.6755 (p) REVERT: Q 109 LEU cc_start: 0.8371 (mt) cc_final: 0.8129 (mm) REVERT: R 25 ASN cc_start: 0.7731 (m-40) cc_final: 0.7447 (m110) outliers start: 3 outliers final: 2 residues processed: 97 average time/residue: 0.4307 time to fit residues: 52.1233 Evaluate side-chains 89 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain O residue 64 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 56 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN O 104 GLN P 64 ASN Q 68 GLN R 75 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.126921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.108672 restraints weight = 11084.933| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 0.70 r_work: 0.3323 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8965 Z= 0.185 Angle : 0.582 4.959 12971 Z= 0.350 Chirality : 0.036 0.140 1475 Planarity : 0.005 0.031 936 Dihedral : 31.679 89.818 2801 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.90 % Allowed : 8.13 % Favored : 90.97 % 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: 1.63 (0.35), residues: 517 helix: 1.53 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -0.17 (0.46), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS N 75 PHE 0.016 0.002 PHE P 62 TYR 0.021 0.002 TYR N 88 ARG 0.005 0.001 ARG N 55 Details of bonding type rmsd hydrogen bonds : bond 0.04195 ( 425) hydrogen bonds : angle 3.34267 ( 1113) covalent geometry : bond 0.00408 ( 8965) covalent geometry : angle 0.58173 (12971) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.569 Fit side-chains REVERT: N 92 ARG cc_start: 0.7077 (mtp85) cc_final: 0.6770 (mtp85) REVERT: P 68 GLU cc_start: 0.7007 (mt-10) cc_final: 0.6775 (mt-10) REVERT: Q 64 LYS cc_start: 0.7315 (mtmt) cc_final: 0.6949 (mtpt) REVERT: Q 109 LEU cc_start: 0.8365 (mt) cc_final: 0.8085 (mm) REVERT: R 25 ASN cc_start: 0.7751 (m-40) cc_final: 0.7453 (m110) outliers start: 4 outliers final: 3 residues processed: 96 average time/residue: 0.3712 time to fit residues: 43.1729 Evaluate side-chains 84 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 104 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 48 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 40 optimal weight: 0.1980 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 54 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN R 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.125804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.107392 restraints weight = 11033.690| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 0.74 r_work: 0.3301 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8965 Z= 0.199 Angle : 0.593 4.836 12971 Z= 0.354 Chirality : 0.037 0.148 1475 Planarity : 0.005 0.034 936 Dihedral : 31.559 89.230 2801 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.03 % Allowed : 10.16 % Favored : 87.81 % 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: 1.70 (0.35), residues: 517 helix: 1.58 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -0.10 (0.48), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS N 75 PHE 0.013 0.002 PHE R 100 TYR 0.045 0.003 TYR N 88 ARG 0.006 0.001 ARG O 20 Details of bonding type rmsd hydrogen bonds : bond 0.04261 ( 425) hydrogen bonds : angle 3.34305 ( 1113) covalent geometry : bond 0.00445 ( 8965) covalent geometry : angle 0.59262 (12971) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.601 Fit side-chains REVERT: N 92 ARG cc_start: 0.7154 (mtp85) cc_final: 0.6824 (mtp85) REVERT: Q 53 ARG cc_start: 0.7653 (ttp-170) cc_final: 0.7426 (ttp-170) REVERT: Q 64 LYS cc_start: 0.7396 (mttt) cc_final: 0.7008 (mtpt) REVERT: Q 109 LEU cc_start: 0.8357 (mt) cc_final: 0.8057 (mm) REVERT: R 25 ASN cc_start: 0.7813 (m-40) cc_final: 0.7357 (m110) outliers start: 9 outliers final: 8 residues processed: 90 average time/residue: 0.4051 time to fit residues: 44.7636 Evaluate side-chains 90 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain R residue 95 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 14 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 0.1980 chunk 29 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.126691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.108357 restraints weight = 11004.248| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 0.74 r_work: 0.3316 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8965 Z= 0.168 Angle : 0.564 4.884 12971 Z= 0.341 Chirality : 0.035 0.146 1475 Planarity : 0.004 0.034 936 Dihedral : 31.446 91.353 2801 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.03 % Allowed : 10.84 % Favored : 87.13 % 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: 2.01 (0.36), residues: 517 helix: 1.85 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -0.17 (0.49), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 75 PHE 0.011 0.002 PHE P 62 TYR 0.061 0.002 TYR N 88 ARG 0.003 0.000 ARG O 20 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 425) hydrogen bonds : angle 3.24497 ( 1113) covalent geometry : bond 0.00365 ( 8965) covalent geometry : angle 0.56353 (12971) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.632 Fit side-chains REVERT: N 92 ARG cc_start: 0.7149 (mtp85) cc_final: 0.6808 (mtp85) REVERT: P 82 LYS cc_start: 0.7878 (mtmm) cc_final: 0.7406 (mttm) REVERT: Q 64 LYS cc_start: 0.7289 (mttt) cc_final: 0.6906 (mtpt) REVERT: R 25 ASN cc_start: 0.7804 (m-40) cc_final: 0.7364 (m110) outliers start: 9 outliers final: 7 residues processed: 89 average time/residue: 0.3501 time to fit residues: 38.3433 Evaluate side-chains 89 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain R residue 95 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 26 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.125406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.107916 restraints weight = 11134.310| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 0.70 r_work: 0.3313 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8965 Z= 0.188 Angle : 0.577 4.873 12971 Z= 0.347 Chirality : 0.036 0.142 1475 Planarity : 0.004 0.034 936 Dihedral : 31.254 89.565 2801 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.03 % Allowed : 12.42 % Favored : 85.55 % 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: 1.91 (0.35), residues: 517 helix: 1.78 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -0.20 (0.50), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 75 PHE 0.011 0.002 PHE R 100 TYR 0.061 0.003 TYR N 88 ARG 0.002 0.000 ARG Q 53 Details of bonding type rmsd hydrogen bonds : bond 0.04060 ( 425) hydrogen bonds : angle 3.29536 ( 1113) covalent geometry : bond 0.00418 ( 8965) covalent geometry : angle 0.57658 (12971) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.649 Fit side-chains REVERT: P 82 LYS cc_start: 0.7783 (mtmm) cc_final: 0.7310 (mttm) REVERT: R 25 ASN cc_start: 0.7815 (m-40) cc_final: 0.7361 (m110) outliers start: 9 outliers final: 8 residues processed: 91 average time/residue: 0.3598 time to fit residues: 39.8759 Evaluate side-chains 92 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 71 VAL Chi-restraints excluded: chain R residue 95 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 67 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN R 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.125900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.108891 restraints weight = 11170.419| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 0.66 r_work: 0.3329 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8965 Z= 0.185 Angle : 0.567 4.994 12971 Z= 0.340 Chirality : 0.035 0.148 1475 Planarity : 0.004 0.034 936 Dihedral : 31.046 92.066 2801 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.03 % Allowed : 11.74 % Favored : 86.23 % 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: 1.95 (0.35), residues: 517 helix: 1.81 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -0.20 (0.50), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 75 PHE 0.012 0.002 PHE R 100 TYR 0.049 0.002 TYR N 88 ARG 0.006 0.000 ARG Q 53 Details of bonding type rmsd hydrogen bonds : bond 0.03960 ( 425) hydrogen bonds : angle 3.27182 ( 1113) covalent geometry : bond 0.00409 ( 8965) covalent geometry : angle 0.56659 (12971) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.570 Fit side-chains REVERT: N 92 ARG cc_start: 0.7089 (mtp85) cc_final: 0.6751 (mtp85) REVERT: P 68 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6766 (mt-10) REVERT: P 82 LYS cc_start: 0.7801 (mtmm) cc_final: 0.7357 (mttm) REVERT: R 25 ASN cc_start: 0.7811 (m-40) cc_final: 0.7384 (m110) outliers start: 9 outliers final: 8 residues processed: 93 average time/residue: 0.3532 time to fit residues: 39.9351 Evaluate side-chains 90 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain R residue 95 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 7 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 29 optimal weight: 0.0060 chunk 6 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN R 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.126329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.108993 restraints weight = 11125.403| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 0.69 r_work: 0.3327 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8965 Z= 0.169 Angle : 0.564 7.915 12971 Z= 0.337 Chirality : 0.034 0.146 1475 Planarity : 0.004 0.044 936 Dihedral : 31.020 92.130 2801 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.26 % Allowed : 12.87 % Favored : 84.88 % 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: 2.10 (0.36), residues: 517 helix: 1.92 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -0.19 (0.50), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 75 PHE 0.012 0.002 PHE R 100 TYR 0.063 0.003 TYR N 88 ARG 0.006 0.000 ARG Q 53 Details of bonding type rmsd hydrogen bonds : bond 0.03847 ( 425) hydrogen bonds : angle 3.23807 ( 1113) covalent geometry : bond 0.00369 ( 8965) covalent geometry : angle 0.56381 (12971) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.659 Fit side-chains REVERT: N 92 ARG cc_start: 0.7090 (mtp85) cc_final: 0.6743 (mtp85) REVERT: P 68 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6747 (mt-10) REVERT: P 82 LYS cc_start: 0.7813 (mtmm) cc_final: 0.7367 (mttm) REVERT: R 25 ASN cc_start: 0.7802 (m-40) cc_final: 0.7361 (m110) outliers start: 10 outliers final: 9 residues processed: 87 average time/residue: 0.3804 time to fit residues: 41.2177 Evaluate side-chains 91 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain R residue 95 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN R 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.126103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.109012 restraints weight = 11250.589| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 0.66 r_work: 0.3332 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8965 Z= 0.182 Angle : 0.569 7.290 12971 Z= 0.340 Chirality : 0.035 0.155 1475 Planarity : 0.004 0.034 936 Dihedral : 30.894 92.213 2801 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.48 % Allowed : 12.87 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.03 (0.36), residues: 517 helix: 1.87 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -0.16 (0.50), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 75 PHE 0.012 0.002 PHE R 100 TYR 0.021 0.002 TYR N 88 ARG 0.005 0.000 ARG Q 53 Details of bonding type rmsd hydrogen bonds : bond 0.03943 ( 425) hydrogen bonds : angle 3.28196 ( 1113) covalent geometry : bond 0.00403 ( 8965) covalent geometry : angle 0.56895 (12971) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.570 Fit side-chains REVERT: N 92 ARG cc_start: 0.7087 (mtp85) cc_final: 0.6747 (mtp85) REVERT: P 68 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6738 (mt-10) REVERT: P 82 LYS cc_start: 0.7771 (mtmm) cc_final: 0.7347 (mttm) REVERT: R 25 ASN cc_start: 0.7799 (m-40) cc_final: 0.7341 (m110) outliers start: 11 outliers final: 11 residues processed: 89 average time/residue: 0.3423 time to fit residues: 37.1991 Evaluate side-chains 93 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 95 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 22 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN R 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.126132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.109098 restraints weight = 11080.184| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 0.65 r_work: 0.3335 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8965 Z= 0.182 Angle : 0.567 6.759 12971 Z= 0.339 Chirality : 0.035 0.148 1475 Planarity : 0.004 0.035 936 Dihedral : 30.811 92.581 2801 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.48 % Allowed : 12.42 % Favored : 85.10 % 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: 2.00 (0.35), residues: 517 helix: 1.84 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -0.17 (0.50), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 75 PHE 0.011 0.002 PHE R 100 TYR 0.015 0.002 TYR N 88 ARG 0.005 0.000 ARG Q 53 Details of bonding type rmsd hydrogen bonds : bond 0.03943 ( 425) hydrogen bonds : angle 3.27024 ( 1113) covalent geometry : bond 0.00402 ( 8965) covalent geometry : angle 0.56713 (12971) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.589 Fit side-chains REVERT: N 92 ARG cc_start: 0.7096 (mtp85) cc_final: 0.6738 (mtp85) REVERT: P 68 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6786 (mt-10) REVERT: P 82 LYS cc_start: 0.7728 (mtmm) cc_final: 0.7312 (mttm) REVERT: R 25 ASN cc_start: 0.7804 (m-40) cc_final: 0.7356 (m110) outliers start: 11 outliers final: 11 residues processed: 84 average time/residue: 0.3362 time to fit residues: 34.7023 Evaluate side-chains 89 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 95 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.126308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.109673 restraints weight = 11150.973| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 0.63 r_work: 0.3346 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8965 Z= 0.181 Angle : 0.566 6.569 12971 Z= 0.339 Chirality : 0.035 0.144 1475 Planarity : 0.005 0.052 936 Dihedral : 30.804 92.889 2801 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.93 % Allowed : 12.19 % Favored : 84.88 % 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: 2.04 (0.36), residues: 517 helix: 1.87 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -0.16 (0.50), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 75 PHE 0.010 0.002 PHE R 100 TYR 0.014 0.002 TYR N 88 ARG 0.004 0.000 ARG Q 53 Details of bonding type rmsd hydrogen bonds : bond 0.03912 ( 425) hydrogen bonds : angle 3.26924 ( 1113) covalent geometry : bond 0.00399 ( 8965) covalent geometry : angle 0.56615 (12971) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5205.73 seconds wall clock time: 90 minutes 45.59 seconds (5445.59 seconds total)