Starting phenix.real_space_refine on Mon Sep 23 12:54:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cu8_7619/09_2024/6cu8_7619.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cu8_7619/09_2024/6cu8_7619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cu8_7619/09_2024/6cu8_7619.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cu8_7619/09_2024/6cu8_7619.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cu8_7619/09_2024/6cu8_7619.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cu8_7619/09_2024/6cu8_7619.cif" } resolution = 3.6 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 ------------------------------------------------------------------------------- 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= 0.002 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: 3 Type Number sf(0) Gaussians C 1780 2.51 5 N 510 2.21 5 O 590 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-5461/modules/chem_data/mon_lib" Total number of atoms: 2880 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 288 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 1.03, per 1000 atoms: 0.36 Number of scatterers: 2880 At special positions: 0 Unit cell: (96.3, 68.48, 44.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 590 8.00 N 510 7.00 C 1780 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: 0.57 Conformation dependent library (CDL) restraints added in 329.0 milliseconds 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 720 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 49 removed outlier: 6.999A pdb=" N LYS A 45 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N VAL C 48 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLY A 47 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLU E 46 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LYS E 45 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N VAL G 48 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N GLY E 47 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LYS G 45 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N VAL I 48 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY G 47 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 77 removed outlier: 6.457A pdb=" N ALA E 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 81 through 82 Processing sheet with id=AA4, first strand: chain 'B' and resid 45 through 49 removed outlier: 6.939A pdb=" N LYS B 45 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N VAL D 48 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLY B 47 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LYS D 45 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N VAL F 48 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLY D 47 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LYS F 45 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N VAL H 48 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLY F 47 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LYS H 45 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N VAL J 48 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLY H 47 " --> pdb=" O VAL J 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 77 Processing sheet with id=AA6, first strand: chain 'B' and resid 81 through 82 removed outlier: 6.567A pdb=" N THR B 81 " --> pdb=" O VAL D 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'F' and resid 61 through 63 Processing sheet with id=AA8, first strand: chain 'F' and resid 81 through 82 removed outlier: 6.601A pdb=" N THR F 81 " --> pdb=" O VAL H 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 81 through 82 removed outlier: 6.633A pdb=" N THR G 81 " --> pdb=" O VAL I 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 13 hydrogen bonds defined for protein. 39 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: 0.54 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 520 1.29 - 1.35: 452 1.35 - 1.42: 28 1.42 - 1.48: 480 1.48 - 1.55: 1400 Bond restraints: 2880 Sorted by residual: bond pdb=" CB ASN A 65 " pdb=" CG ASN A 65 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.18e+00 bond pdb=" CB ASN D 65 " pdb=" CG ASN D 65 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.17e+00 bond pdb=" CB ASN I 65 " pdb=" CG ASN I 65 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.16e+00 bond pdb=" CB ASN F 65 " pdb=" CG ASN F 65 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.15e+00 bond pdb=" CB ASN E 65 " pdb=" CG ASN E 65 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.14e+00 ... (remaining 2875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.69: 2928 0.69 - 1.39: 760 1.39 - 2.08: 112 2.08 - 2.78: 80 2.78 - 3.47: 20 Bond angle restraints: 3900 Sorted by residual: angle pdb=" C GLU G 57 " pdb=" N LYS G 58 " pdb=" CA LYS G 58 " ideal model delta sigma weight residual 122.19 124.91 -2.72 1.41e+00 5.03e-01 3.72e+00 angle pdb=" C GLY E 51 " pdb=" N VAL E 52 " pdb=" CA VAL E 52 " ideal model delta sigma weight residual 121.97 125.44 -3.47 1.80e+00 3.09e-01 3.72e+00 angle pdb=" C GLY C 51 " pdb=" N VAL C 52 " pdb=" CA VAL C 52 " ideal model delta sigma weight residual 121.97 125.43 -3.46 1.80e+00 3.09e-01 3.70e+00 angle pdb=" C GLY I 51 " pdb=" N VAL I 52 " pdb=" CA VAL I 52 " ideal model delta sigma weight residual 121.97 125.42 -3.45 1.80e+00 3.09e-01 3.68e+00 angle pdb=" C GLU B 57 " pdb=" N LYS B 58 " pdb=" CA LYS B 58 " ideal model delta sigma weight residual 122.19 124.89 -2.70 1.41e+00 5.03e-01 3.67e+00 ... (remaining 3895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 4.30: 1190 4.30 - 8.59: 260 8.59 - 12.88: 141 12.88 - 17.18: 99 17.18 - 21.47: 30 Dihedral angle restraints: 1720 sinusoidal: 600 harmonic: 1120 Sorted by residual: dihedral pdb=" CA VAL C 74 " pdb=" C VAL C 74 " pdb=" N THR C 75 " pdb=" CA THR C 75 " ideal model delta harmonic sigma weight residual 180.00 161.09 18.91 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA VAL E 74 " pdb=" C VAL E 74 " pdb=" N THR E 75 " pdb=" CA THR E 75 " ideal model delta harmonic sigma weight residual 180.00 161.12 18.88 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA VAL B 74 " pdb=" C VAL B 74 " pdb=" N THR B 75 " pdb=" CA THR B 75 " ideal model delta harmonic sigma weight residual 180.00 161.13 18.87 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 1717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 317 0.033 - 0.066: 86 0.066 - 0.099: 44 0.099 - 0.132: 65 0.132 - 0.165: 28 Chirality restraints: 540 Sorted by residual: chirality pdb=" CA VAL D 52 " pdb=" N VAL D 52 " pdb=" C VAL D 52 " pdb=" CB VAL D 52 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CA VAL H 52 " pdb=" N VAL H 52 " pdb=" C VAL H 52 " pdb=" CB VAL H 52 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.67e-01 chirality pdb=" CA VAL J 52 " pdb=" N VAL J 52 " pdb=" C VAL J 52 " pdb=" CB VAL J 52 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.62e-01 ... (remaining 537 not shown) Planarity restraints: 480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN G 79 " -0.004 2.00e-02 2.50e+03 7.48e-03 5.59e-01 pdb=" CD GLN G 79 " 0.013 2.00e-02 2.50e+03 pdb=" OE1 GLN G 79 " -0.005 2.00e-02 2.50e+03 pdb=" NE2 GLN G 79 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 79 " -0.004 2.00e-02 2.50e+03 7.43e-03 5.53e-01 pdb=" CD GLN A 79 " 0.013 2.00e-02 2.50e+03 pdb=" OE1 GLN A 79 " -0.005 2.00e-02 2.50e+03 pdb=" NE2 GLN A 79 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN E 79 " -0.004 2.00e-02 2.50e+03 7.41e-03 5.49e-01 pdb=" CD GLN E 79 " 0.013 2.00e-02 2.50e+03 pdb=" OE1 GLN E 79 " -0.005 2.00e-02 2.50e+03 pdb=" NE2 GLN E 79 " -0.004 2.00e-02 2.50e+03 ... (remaining 477 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 1138 2.91 - 3.41: 2277 3.41 - 3.90: 4694 3.90 - 4.40: 4410 4.40 - 4.90: 9453 Nonbonded interactions: 21972 Sorted by model distance: nonbonded pdb=" N ASN B 65 " pdb=" OD1 ASN B 65 " model vdw 2.412 3.120 nonbonded pdb=" N ASN J 65 " pdb=" OD1 ASN J 65 " model vdw 2.412 3.120 nonbonded pdb=" N ASN H 65 " pdb=" OD1 ASN H 65 " model vdw 2.412 3.120 nonbonded pdb=" N ASN C 65 " pdb=" OD1 ASN C 65 " model vdw 2.412 3.120 nonbonded pdb=" N ASN F 65 " pdb=" OD1 ASN F 65 " model vdw 2.412 3.120 ... (remaining 21967 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' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.310 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.540 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2880 Z= 0.252 Angle : 0.726 3.470 3900 Z= 0.430 Chirality : 0.062 0.165 540 Planarity : 0.002 0.007 480 Dihedral : 7.746 21.472 1000 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.47), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.36), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.349 Fit side-chains REVERT: A 58 LYS cc_start: 0.8501 (mttp) cc_final: 0.7794 (pttm) REVERT: I 75 THR cc_start: 0.7029 (m) cc_final: 0.6813 (p) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1125 time to fit residues: 15.4533 Evaluate side-chains 69 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 16 optimal weight: 40.0000 chunk 10 optimal weight: 0.0980 chunk 20 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 12 optimal weight: 40.0000 chunk 19 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 overall best weight: 5.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 GLN D 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2880 Z= 0.214 Angle : 0.685 3.481 3900 Z= 0.409 Chirality : 0.053 0.122 540 Planarity : 0.003 0.011 480 Dihedral : 6.877 15.655 400 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 1.61 % Allowed : 12.58 % Favored : 85.81 % 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: -2.69 (0.44), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.34), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.330 Fit side-chains REVERT: A 58 LYS cc_start: 0.8396 (mttp) cc_final: 0.7824 (pttm) REVERT: A 61 GLU cc_start: 0.7504 (pm20) cc_final: 0.5990 (mm-30) REVERT: B 61 GLU cc_start: 0.6961 (pt0) cc_final: 0.5949 (mm-30) outliers start: 5 outliers final: 3 residues processed: 71 average time/residue: 0.0809 time to fit residues: 7.7711 Evaluate side-chains 59 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain F residue 81 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 36 optimal weight: 30.0000 chunk 39 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 12 optimal weight: 30.0000 chunk 29 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 overall best weight: 8.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 2880 Z= 0.350 Angle : 0.765 4.249 3900 Z= 0.457 Chirality : 0.057 0.124 540 Planarity : 0.003 0.014 480 Dihedral : 7.556 17.288 400 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 3.23 % Allowed : 14.19 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.37), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.326 Fit side-chains REVERT: A 61 GLU cc_start: 0.7694 (pm20) cc_final: 0.5914 (mm-30) REVERT: A 79 GLN cc_start: 0.8831 (tt0) cc_final: 0.8509 (tt0) REVERT: B 61 GLU cc_start: 0.7169 (pt0) cc_final: 0.6270 (tp30) REVERT: J 46 GLU cc_start: 0.6289 (tt0) cc_final: 0.5913 (tt0) outliers start: 10 outliers final: 4 residues processed: 65 average time/residue: 0.1016 time to fit residues: 8.5335 Evaluate side-chains 44 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain F residue 81 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 24 optimal weight: 40.0000 chunk 36 optimal weight: 6.9990 chunk 38 optimal weight: 20.0000 chunk 19 optimal weight: 30.0000 chunk 34 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2880 Z= 0.326 Angle : 0.719 4.152 3900 Z= 0.429 Chirality : 0.057 0.128 540 Planarity : 0.003 0.013 480 Dihedral : 7.255 16.471 400 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 3.87 % Allowed : 16.45 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.36), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.27), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 50 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 42 time to evaluate : 0.336 Fit side-chains REVERT: A 61 GLU cc_start: 0.7799 (pm20) cc_final: 0.5999 (mm-30) REVERT: B 61 GLU cc_start: 0.7123 (pt0) cc_final: 0.6164 (tp30) outliers start: 12 outliers final: 9 residues processed: 52 average time/residue: 0.0817 time to fit residues: 5.9769 Evaluate side-chains 49 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain J residue 81 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 30.0000 chunk 15 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 19 optimal weight: 30.0000 chunk 34 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 GLN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.5012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2880 Z= 0.268 Angle : 0.662 3.933 3900 Z= 0.393 Chirality : 0.056 0.128 540 Planarity : 0.003 0.011 480 Dihedral : 6.902 15.618 400 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 5.48 % Allowed : 15.48 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.37), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 50 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 41 time to evaluate : 0.324 Fit side-chains REVERT: A 57 GLU cc_start: 0.3733 (OUTLIER) cc_final: 0.1963 (pm20) REVERT: A 61 GLU cc_start: 0.7772 (pm20) cc_final: 0.5906 (mm-30) REVERT: B 57 GLU cc_start: 0.3966 (OUTLIER) cc_final: 0.3122 (pt0) REVERT: B 61 GLU cc_start: 0.7059 (pt0) cc_final: 0.6022 (mm-30) outliers start: 17 outliers final: 10 residues processed: 56 average time/residue: 0.0842 time to fit residues: 6.4791 Evaluate side-chains 51 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 39 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain J residue 81 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.0570 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 17 optimal weight: 8.9990 chunk 3 optimal weight: 40.0000 chunk 12 optimal weight: 30.0000 chunk 20 optimal weight: 40.0000 chunk 37 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 overall best weight: 4.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 79 GLN ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2880 Z= 0.183 Angle : 0.593 3.275 3900 Z= 0.350 Chirality : 0.055 0.125 540 Planarity : 0.002 0.013 480 Dihedral : 6.279 14.035 400 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 4.84 % Allowed : 15.48 % Favored : 79.68 % 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: -2.65 (0.40), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 50 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 48 time to evaluate : 0.334 Fit side-chains REVERT: A 57 GLU cc_start: 0.3893 (OUTLIER) cc_final: 0.1982 (pm20) REVERT: A 61 GLU cc_start: 0.7710 (pm20) cc_final: 0.5861 (mm-30) REVERT: B 57 GLU cc_start: 0.3798 (OUTLIER) cc_final: 0.3047 (pt0) REVERT: B 61 GLU cc_start: 0.7060 (pt0) cc_final: 0.6069 (mm-30) outliers start: 15 outliers final: 10 residues processed: 58 average time/residue: 0.0787 time to fit residues: 6.5102 Evaluate side-chains 55 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 43 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain J residue 81 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 20.0000 chunk 32 optimal weight: 30.0000 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 19 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2880 Z= 0.293 Angle : 0.670 3.833 3900 Z= 0.396 Chirality : 0.056 0.127 540 Planarity : 0.003 0.015 480 Dihedral : 6.775 15.529 400 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 6.77 % Allowed : 16.13 % Favored : 77.10 % 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: -2.97 (0.37), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 41 time to evaluate : 0.321 Fit side-chains REVERT: A 57 GLU cc_start: 0.3899 (OUTLIER) cc_final: 0.2046 (pm20) REVERT: A 61 GLU cc_start: 0.7875 (pm20) cc_final: 0.6045 (mm-30) REVERT: B 57 GLU cc_start: 0.4071 (OUTLIER) cc_final: 0.3264 (pt0) REVERT: B 61 GLU cc_start: 0.7116 (pt0) cc_final: 0.6072 (mm-30) outliers start: 21 outliers final: 13 residues processed: 57 average time/residue: 0.0797 time to fit residues: 6.3040 Evaluate side-chains 53 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 38 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain J residue 81 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 36 optimal weight: 30.0000 chunk 33 optimal weight: 0.3980 chunk 21 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 11 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 overall best weight: 6.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2880 Z= 0.246 Angle : 0.653 5.945 3900 Z= 0.384 Chirality : 0.056 0.126 540 Planarity : 0.003 0.015 480 Dihedral : 6.609 14.956 400 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 6.45 % Allowed : 16.13 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.37), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 50 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 37 time to evaluate : 0.290 Fit side-chains REVERT: A 57 GLU cc_start: 0.4069 (OUTLIER) cc_final: 0.2193 (pm20) REVERT: A 61 GLU cc_start: 0.7815 (pm20) cc_final: 0.6052 (mm-30) REVERT: B 57 GLU cc_start: 0.4016 (OUTLIER) cc_final: 0.3296 (pt0) REVERT: B 61 GLU cc_start: 0.7077 (pt0) cc_final: 0.6067 (mm-30) outliers start: 20 outliers final: 13 residues processed: 52 average time/residue: 0.0822 time to fit residues: 5.9734 Evaluate side-chains 52 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 37 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain J residue 81 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 24 optimal weight: 30.0000 chunk 19 optimal weight: 5.9990 chunk 25 optimal weight: 30.0000 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.5534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2880 Z= 0.234 Angle : 0.662 6.754 3900 Z= 0.386 Chirality : 0.056 0.125 540 Planarity : 0.003 0.016 480 Dihedral : 6.461 14.818 400 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 4.84 % Allowed : 17.42 % Favored : 77.74 % 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: -2.86 (0.38), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 40 time to evaluate : 0.319 Fit side-chains REVERT: A 57 GLU cc_start: 0.4014 (OUTLIER) cc_final: 0.2171 (pm20) REVERT: A 61 GLU cc_start: 0.7846 (pm20) cc_final: 0.5999 (mm-30) REVERT: B 57 GLU cc_start: 0.4035 (OUTLIER) cc_final: 0.3259 (pt0) REVERT: B 61 GLU cc_start: 0.7084 (pt0) cc_final: 0.6095 (mm-30) outliers start: 15 outliers final: 13 residues processed: 52 average time/residue: 0.0671 time to fit residues: 5.1198 Evaluate side-chains 55 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 40 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain J residue 81 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 20.0000 chunk 9 optimal weight: 0.0470 chunk 29 optimal weight: 7.9990 chunk 4 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 32 optimal weight: 0.0970 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 overall best weight: 4.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.5594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2880 Z= 0.195 Angle : 0.627 6.387 3900 Z= 0.365 Chirality : 0.055 0.125 540 Planarity : 0.003 0.016 480 Dihedral : 6.146 14.258 400 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 5.16 % Allowed : 17.42 % Favored : 77.42 % 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: -2.66 (0.40), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS F 50 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 44 time to evaluate : 0.333 Fit side-chains REVERT: A 57 GLU cc_start: 0.3888 (OUTLIER) cc_final: 0.2098 (pm20) REVERT: A 61 GLU cc_start: 0.7865 (pm20) cc_final: 0.5999 (mm-30) REVERT: B 57 GLU cc_start: 0.4056 (OUTLIER) cc_final: 0.3310 (pt0) REVERT: B 61 GLU cc_start: 0.7040 (pt0) cc_final: 0.6105 (mm-30) outliers start: 16 outliers final: 11 residues processed: 54 average time/residue: 0.0666 time to fit residues: 5.2948 Evaluate side-chains 54 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 41 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain J residue 81 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 20.0000 chunk 36 optimal weight: 40.0000 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 30.0000 chunk 23 optimal weight: 20.0000 chunk 15 optimal weight: 40.0000 chunk 14 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 overall best weight: 5.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.118276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.104707 restraints weight = 7068.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.107122 restraints weight = 3506.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.108675 restraints weight = 2203.106| |-----------------------------------------------------------------------------| r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.5662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2880 Z= 0.233 Angle : 0.656 6.085 3900 Z= 0.381 Chirality : 0.055 0.124 540 Planarity : 0.003 0.017 480 Dihedral : 6.282 14.568 400 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 4.84 % Allowed : 18.06 % Favored : 77.10 % 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: -2.78 (0.39), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 50 =============================================================================== Job complete usr+sys time: 804.56 seconds wall clock time: 15 minutes 11.01 seconds (911.01 seconds total)