Starting phenix.real_space_refine on Mon Sep 23 14:50:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adu_15370/09_2024/8adu_15370.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adu_15370/09_2024/8adu_15370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adu_15370/09_2024/8adu_15370.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adu_15370/09_2024/8adu_15370.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adu_15370/09_2024/8adu_15370.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adu_15370/09_2024/8adu_15370.cif" } resolution = 3.24 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 2160 2.51 5 N 600 2.21 5 O 690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3460 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Restraints were copied for chains: C, B, E, D Time building chain proxies: 2.04, per 1000 atoms: 0.59 Number of scatterers: 3460 At special positions: 0 Unit cell: (86.1, 97.65, 39.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 690 8.00 N 600 7.00 C 2160 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: 0.88 Conformation dependent library (CDL) restraints added in 461.7 milliseconds 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 850 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 20 removed outlier: 6.880A pdb=" N ALA A 17 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N GLU B 20 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA A 19 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA B 17 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N GLU C 20 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA B 19 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA C 17 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N GLU D 20 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA C 19 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA D 17 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N GLU E 20 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA D 19 " --> pdb=" O GLU E 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 31 Processing sheet with id=AA3, first strand: chain 'A' and resid 38 through 40 Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 54 Processing sheet with id=AA5, first strand: chain 'A' and resid 61 through 66 removed outlier: 6.207A pdb=" N GLN A 62 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ASN B 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR A 64 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLN B 62 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ASN C 65 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR B 64 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLN C 62 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ASN D 65 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR C 64 " --> pdb=" O ASN D 65 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLN D 62 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ASN E 65 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N THR D 64 " --> pdb=" O ASN E 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 69 through 71 Processing sheet with id=AA7, first strand: chain 'A' and resid 75 through 78 Processing sheet with id=AA8, first strand: chain 'A' and resid 92 through 94 76 hydrogen bonds defined for protein. 228 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.79 Time building geometry restraints manager: 1.02 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: 1145 1.34 - 1.45: 439 1.45 - 1.57: 1871 1.57 - 1.69: 0 1.69 - 1.80: 20 Bond restraints: 3475 Sorted by residual: bond pdb=" CB VAL E 15 " pdb=" CG2 VAL E 15 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.70e+00 bond pdb=" CB VAL A 15 " pdb=" CG2 VAL A 15 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.69e+00 bond pdb=" CB VAL D 15 " pdb=" CG2 VAL D 15 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.67e+00 bond pdb=" CB VAL C 15 " pdb=" CG2 VAL C 15 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.67e+00 bond pdb=" CB VAL B 15 " pdb=" CG2 VAL B 15 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.66e+00 ... (remaining 3470 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.88: 3777 0.88 - 1.77: 660 1.77 - 2.65: 153 2.65 - 3.53: 45 3.53 - 4.42: 25 Bond angle restraints: 4660 Sorted by residual: angle pdb=" CA GLN D 79 " pdb=" CB GLN D 79 " pdb=" CG GLN D 79 " ideal model delta sigma weight residual 114.10 118.52 -4.42 2.00e+00 2.50e-01 4.87e+00 angle pdb=" CA GLN A 79 " pdb=" CB GLN A 79 " pdb=" CG GLN A 79 " ideal model delta sigma weight residual 114.10 118.51 -4.41 2.00e+00 2.50e-01 4.86e+00 angle pdb=" C GLN E 79 " pdb=" CA GLN E 79 " pdb=" CB GLN E 79 " ideal model delta sigma weight residual 110.42 114.81 -4.39 1.99e+00 2.53e-01 4.86e+00 angle pdb=" CA GLN C 79 " pdb=" CB GLN C 79 " pdb=" CG GLN C 79 " ideal model delta sigma weight residual 114.10 118.50 -4.40 2.00e+00 2.50e-01 4.85e+00 angle pdb=" C GLN C 79 " pdb=" CA GLN C 79 " pdb=" CB GLN C 79 " ideal model delta sigma weight residual 110.42 114.80 -4.38 1.99e+00 2.53e-01 4.85e+00 ... (remaining 4655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 1904 17.35 - 34.69: 136 34.69 - 52.03: 30 52.03 - 69.38: 5 69.38 - 86.72: 15 Dihedral angle restraints: 2090 sinusoidal: 745 harmonic: 1345 Sorted by residual: dihedral pdb=" CA MET E 5 " pdb=" C MET E 5 " pdb=" N LYS E 6 " pdb=" CA LYS E 6 " ideal model delta harmonic sigma weight residual 180.00 -160.26 -19.74 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA MET D 5 " pdb=" C MET D 5 " pdb=" N LYS D 6 " pdb=" CA LYS D 6 " ideal model delta harmonic sigma weight residual -180.00 -160.27 -19.73 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA MET C 5 " pdb=" C MET C 5 " pdb=" N LYS C 6 " pdb=" CA LYS C 6 " ideal model delta harmonic sigma weight residual -180.00 -160.27 -19.73 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 2087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 505 0.087 - 0.173: 65 0.173 - 0.260: 5 0.260 - 0.347: 0 0.347 - 0.433: 5 Chirality restraints: 580 Sorted by residual: chirality pdb=" CB VAL D 15 " pdb=" CA VAL D 15 " pdb=" CG1 VAL D 15 " pdb=" CG2 VAL D 15 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.70e+00 chirality pdb=" CB VAL E 15 " pdb=" CA VAL E 15 " pdb=" CG1 VAL E 15 " pdb=" CG2 VAL E 15 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.65e+00 chirality pdb=" CB VAL B 15 " pdb=" CA VAL B 15 " pdb=" CG1 VAL B 15 " pdb=" CG2 VAL B 15 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.65e+00 ... (remaining 577 not shown) Planarity restraints: 585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 4 " -0.010 2.00e-02 2.50e+03 9.37e-03 1.54e+00 pdb=" CG PHE E 4 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE E 4 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE E 4 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE E 4 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 4 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE E 4 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 4 " -0.010 2.00e-02 2.50e+03 9.22e-03 1.49e+00 pdb=" CG PHE D 4 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE D 4 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE D 4 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE D 4 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 4 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE D 4 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 4 " -0.010 2.00e-02 2.50e+03 9.20e-03 1.48e+00 pdb=" CG PHE C 4 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE C 4 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE C 4 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE C 4 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 4 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 4 " -0.003 2.00e-02 2.50e+03 ... (remaining 582 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1071 2.82 - 3.34: 3134 3.34 - 3.86: 5731 3.86 - 4.38: 6806 4.38 - 4.90: 13256 Nonbonded interactions: 29998 Sorted by model distance: nonbonded pdb=" OG SER E 9 " pdb=" N LYS E 10 " model vdw 2.296 3.120 nonbonded pdb=" OG SER C 9 " pdb=" N LYS C 10 " model vdw 2.297 3.120 nonbonded pdb=" OG SER D 9 " pdb=" N LYS D 10 " model vdw 2.297 3.120 nonbonded pdb=" OG SER A 9 " pdb=" N LYS A 10 " model vdw 2.297 3.120 nonbonded pdb=" OG SER B 9 " pdb=" N LYS B 10 " model vdw 2.297 3.120 ... (remaining 29993 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.650 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 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 : 0.007 0.057 3475 Z= 0.458 Angle : 0.820 4.415 4660 Z= 0.461 Chirality : 0.068 0.433 580 Planarity : 0.003 0.009 585 Dihedral : 15.523 86.720 1240 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.34 % Favored : 88.66 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: -4.91 (0.25), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.74 (0.19), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.022 0.005 PHE E 4 TYR 0.005 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.7926 (tttm) cc_final: 0.7706 (ttmm) REVERT: B 99 GLN cc_start: 0.4969 (tm-30) cc_final: 0.4709 (tm-30) REVERT: C 12 LYS cc_start: 0.7500 (mptt) cc_final: 0.7264 (mptt) REVERT: C 60 LYS cc_start: 0.7879 (tttm) cc_final: 0.7641 (ttmm) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1477 time to fit residues: 16.2258 Evaluate side-chains 69 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3475 Z= 0.320 Angle : 0.695 7.378 4660 Z= 0.369 Chirality : 0.051 0.172 580 Planarity : 0.003 0.010 585 Dihedral : 5.141 15.745 495 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.78 % Favored : 87.22 % Rotamer: Outliers : 5.51 % Allowed : 15.94 % Favored : 78.55 % 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: -4.47 (0.28), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.21), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.019 0.004 PHE D 4 TYR 0.014 0.002 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 78 time to evaluate : 0.374 Fit side-chains REVERT: A 60 LYS cc_start: 0.8173 (tttm) cc_final: 0.7813 (ttmm) REVERT: A 99 GLN cc_start: 0.5076 (tm-30) cc_final: 0.4843 (tm-30) REVERT: B 60 LYS cc_start: 0.8130 (tttm) cc_final: 0.7784 (ttmm) REVERT: C 60 LYS cc_start: 0.7984 (tttm) cc_final: 0.7702 (ttmm) REVERT: D 60 LYS cc_start: 0.8100 (tttm) cc_final: 0.7730 (ttmm) outliers start: 19 outliers final: 14 residues processed: 88 average time/residue: 0.1402 time to fit residues: 15.3845 Evaluate side-chains 87 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 81 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 44 optimal weight: 0.0970 chunk 36 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 overall best weight: 3.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3475 Z= 0.359 Angle : 0.690 6.539 4660 Z= 0.368 Chirality : 0.051 0.144 580 Planarity : 0.003 0.010 585 Dihedral : 5.241 16.755 495 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.55 % Favored : 88.45 % Rotamer: Outliers : 6.67 % Allowed : 17.39 % Favored : 75.94 % 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: -4.43 (0.28), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.22), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS D 50 PHE 0.020 0.005 PHE B 94 TYR 0.010 0.002 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 78 time to evaluate : 0.400 Fit side-chains REVERT: A 60 LYS cc_start: 0.8161 (tttm) cc_final: 0.7812 (ttmm) REVERT: A 99 GLN cc_start: 0.4930 (tm-30) cc_final: 0.4719 (tm-30) REVERT: B 60 LYS cc_start: 0.8107 (tttm) cc_final: 0.7785 (ttmm) REVERT: C 60 LYS cc_start: 0.7998 (tttm) cc_final: 0.7717 (ttmm) REVERT: D 60 LYS cc_start: 0.8165 (tttm) cc_final: 0.7841 (ttmm) outliers start: 23 outliers final: 16 residues processed: 94 average time/residue: 0.1331 time to fit residues: 15.7018 Evaluate side-chains 88 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 81 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3475 Z= 0.186 Angle : 0.584 6.688 4660 Z= 0.309 Chirality : 0.048 0.136 580 Planarity : 0.002 0.009 585 Dihedral : 4.479 13.835 495 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.37 % Favored : 87.63 % Rotamer: Outliers : 5.22 % Allowed : 18.55 % Favored : 76.23 % 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: -4.35 (0.29), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.22), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.016 0.004 PHE C 94 TYR 0.007 0.002 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 0.405 Fit side-chains REVERT: A 60 LYS cc_start: 0.8173 (tttm) cc_final: 0.7830 (ttmm) REVERT: B 60 LYS cc_start: 0.8085 (tttm) cc_final: 0.7767 (ttmm) REVERT: C 60 LYS cc_start: 0.7961 (tttm) cc_final: 0.7717 (ttmm) REVERT: D 60 LYS cc_start: 0.8110 (tttm) cc_final: 0.7290 (ttmm) REVERT: E 61 GLU cc_start: 0.7293 (mp0) cc_final: 0.6458 (mp0) outliers start: 18 outliers final: 14 residues processed: 95 average time/residue: 0.1521 time to fit residues: 17.5738 Evaluate side-chains 93 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 79 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 59 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 3475 Z= 0.554 Angle : 0.798 7.138 4660 Z= 0.426 Chirality : 0.053 0.170 580 Planarity : 0.004 0.011 585 Dihedral : 5.651 19.358 495 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.55 % Favored : 88.45 % Rotamer: Outliers : 6.67 % Allowed : 17.97 % Favored : 75.36 % 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: -4.41 (0.29), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.22), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.025 0.006 PHE B 94 TYR 0.020 0.005 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 74 time to evaluate : 0.343 Fit side-chains REVERT: A 60 LYS cc_start: 0.8135 (tttm) cc_final: 0.7814 (ttmm) REVERT: B 60 LYS cc_start: 0.8180 (tttm) cc_final: 0.7833 (ttmm) REVERT: C 10 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7472 (mtpt) REVERT: C 46 GLU cc_start: 0.8729 (pm20) cc_final: 0.8486 (pm20) REVERT: C 60 LYS cc_start: 0.8016 (tttm) cc_final: 0.7761 (ttmm) REVERT: D 12 LYS cc_start: 0.7721 (mptt) cc_final: 0.7510 (mptt) REVERT: D 60 LYS cc_start: 0.8173 (tttm) cc_final: 0.7683 (tttm) REVERT: E 10 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7715 (mtpt) outliers start: 23 outliers final: 18 residues processed: 89 average time/residue: 0.1520 time to fit residues: 16.3978 Evaluate side-chains 91 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 71 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 81 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3475 Z= 0.359 Angle : 0.698 6.530 4660 Z= 0.370 Chirality : 0.051 0.143 580 Planarity : 0.003 0.010 585 Dihedral : 5.264 17.664 495 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.75 % Favored : 88.25 % Rotamer: Outliers : 6.38 % Allowed : 20.00 % Favored : 73.62 % 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: -4.39 (0.29), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.22), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.021 0.005 PHE C 94 TYR 0.013 0.003 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 77 time to evaluate : 0.396 Fit side-chains REVERT: A 60 LYS cc_start: 0.8160 (tttm) cc_final: 0.7820 (ttmm) REVERT: B 35 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7919 (tt0) REVERT: B 60 LYS cc_start: 0.8181 (tttm) cc_final: 0.7850 (ttmm) REVERT: C 60 LYS cc_start: 0.8014 (tttm) cc_final: 0.7765 (ttmm) REVERT: D 12 LYS cc_start: 0.7589 (mptt) cc_final: 0.7350 (mptt) REVERT: D 60 LYS cc_start: 0.8127 (tttm) cc_final: 0.7609 (tttm) REVERT: E 10 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7593 (mtpt) outliers start: 22 outliers final: 17 residues processed: 92 average time/residue: 0.1580 time to fit residues: 17.7792 Evaluate side-chains 95 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3475 Z= 0.185 Angle : 0.592 6.869 4660 Z= 0.312 Chirality : 0.049 0.140 580 Planarity : 0.002 0.009 585 Dihedral : 4.453 15.075 495 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.37 % Favored : 87.63 % Rotamer: Outliers : 6.38 % Allowed : 21.74 % Favored : 71.88 % 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: -4.36 (0.29), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.22), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.016 0.004 PHE C 94 TYR 0.008 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 83 time to evaluate : 0.488 Fit side-chains REVERT: A 60 LYS cc_start: 0.8181 (tttm) cc_final: 0.7848 (ttmm) REVERT: A 79 GLN cc_start: 0.6679 (OUTLIER) cc_final: 0.5057 (pt0) REVERT: B 35 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7721 (mt-10) REVERT: B 60 LYS cc_start: 0.8090 (tttm) cc_final: 0.7767 (ttmm) REVERT: C 5 MET cc_start: 0.6553 (ttm) cc_final: 0.6318 (ttt) REVERT: C 60 LYS cc_start: 0.7990 (tttm) cc_final: 0.7734 (ttmm) REVERT: D 60 LYS cc_start: 0.8174 (tttm) cc_final: 0.7185 (tttm) REVERT: E 5 MET cc_start: 0.6879 (ttm) cc_final: 0.6606 (ttt) REVERT: E 61 GLU cc_start: 0.7292 (mp0) cc_final: 0.6669 (mp0) outliers start: 22 outliers final: 17 residues processed: 95 average time/residue: 0.1373 time to fit residues: 16.1504 Evaluate side-chains 100 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 81 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 59 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 8.9990 chunk 4 optimal weight: 0.5980 chunk 34 optimal weight: 9.9990 chunk 39 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 37 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 17 optimal weight: 0.2980 chunk 31 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3475 Z= 0.146 Angle : 0.575 6.817 4660 Z= 0.298 Chirality : 0.049 0.140 580 Planarity : 0.002 0.010 585 Dihedral : 4.047 14.696 495 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.37 % Favored : 87.63 % Rotamer: Outliers : 5.51 % Allowed : 21.45 % Favored : 73.04 % 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: -4.30 (0.29), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.22), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.016 0.004 PHE C 94 TYR 0.005 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 0.396 Fit side-chains REVERT: A 35 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7441 (tt0) REVERT: A 60 LYS cc_start: 0.8178 (tttm) cc_final: 0.7825 (ttmm) REVERT: A 79 GLN cc_start: 0.5539 (OUTLIER) cc_final: 0.4738 (pt0) REVERT: B 60 LYS cc_start: 0.8096 (tttm) cc_final: 0.7591 (tttm) REVERT: C 60 LYS cc_start: 0.7988 (tttm) cc_final: 0.7744 (ttmm) REVERT: D 60 LYS cc_start: 0.8086 (tttm) cc_final: 0.7403 (tttm) REVERT: E 61 GLU cc_start: 0.7315 (mp0) cc_final: 0.6996 (mp0) outliers start: 19 outliers final: 14 residues processed: 99 average time/residue: 0.1472 time to fit residues: 17.9811 Evaluate side-chains 105 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 59 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3475 Z= 0.271 Angle : 0.659 6.940 4660 Z= 0.344 Chirality : 0.050 0.144 580 Planarity : 0.003 0.010 585 Dihedral : 4.469 16.964 495 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.55 % Favored : 88.45 % Rotamer: Outliers : 6.67 % Allowed : 20.87 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.27 (0.30), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.23), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.019 0.004 PHE C 94 TYR 0.020 0.003 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 81 time to evaluate : 0.399 Fit side-chains REVERT: A 60 LYS cc_start: 0.8158 (tttm) cc_final: 0.7812 (ttmm) REVERT: A 79 GLN cc_start: 0.7146 (OUTLIER) cc_final: 0.5080 (pt0) REVERT: B 60 LYS cc_start: 0.8173 (tttm) cc_final: 0.7848 (ttmm) REVERT: C 5 MET cc_start: 0.6617 (ttt) cc_final: 0.6413 (ttt) REVERT: C 60 LYS cc_start: 0.7994 (tttm) cc_final: 0.7751 (ttmm) REVERT: D 60 LYS cc_start: 0.8158 (tttm) cc_final: 0.7618 (tttm) outliers start: 23 outliers final: 18 residues processed: 92 average time/residue: 0.1477 time to fit residues: 16.7850 Evaluate side-chains 98 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 79 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 59 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 0.1980 chunk 21 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 38 optimal weight: 0.1980 chunk 10 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 36 optimal weight: 0.1980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 GLN E 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3475 Z= 0.170 Angle : 0.612 6.944 4660 Z= 0.318 Chirality : 0.049 0.137 580 Planarity : 0.002 0.010 585 Dihedral : 4.174 17.706 495 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.99 % Favored : 87.01 % Rotamer: Outliers : 4.93 % Allowed : 22.61 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.23 (0.30), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.23), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.017 0.004 PHE C 94 TYR 0.010 0.002 TYR A 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 0.360 Fit side-chains REVERT: A 35 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7206 (tt0) REVERT: A 60 LYS cc_start: 0.8181 (tttm) cc_final: 0.7830 (ttmm) REVERT: A 79 GLN cc_start: 0.6322 (OUTLIER) cc_final: 0.4792 (pt0) REVERT: B 60 LYS cc_start: 0.8043 (tttm) cc_final: 0.7689 (ttmm) REVERT: C 60 LYS cc_start: 0.7988 (tttm) cc_final: 0.7743 (ttmm) REVERT: D 60 LYS cc_start: 0.8123 (tttm) cc_final: 0.7439 (tttm) REVERT: E 61 GLU cc_start: 0.7327 (mp0) cc_final: 0.7018 (mp0) outliers start: 17 outliers final: 13 residues processed: 92 average time/residue: 0.1426 time to fit residues: 16.2961 Evaluate side-chains 100 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 59 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 0.0060 chunk 6 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 overall best weight: 2.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 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 = 0.106187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.089326 restraints weight = 5097.357| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.57 r_work: 0.3390 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 3475 Z= 0.314 Angle : 0.707 7.019 4660 Z= 0.369 Chirality : 0.050 0.148 580 Planarity : 0.003 0.010 585 Dihedral : 4.654 19.045 495 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.16 % Favored : 87.84 % Rotamer: Outliers : 5.80 % Allowed : 22.03 % Favored : 72.17 % 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: -4.26 (0.30), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.23), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 50 PHE 0.020 0.005 PHE C 94 TYR 0.014 0.003 TYR A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1258.31 seconds wall clock time: 23 minutes 37.28 seconds (1417.28 seconds total)