Starting phenix.real_space_refine on Sun Mar 10 15:21:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cu8_7619/03_2024/6cu8_7619.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cu8_7619/03_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_7619/03_2024/6cu8_7619.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cu8_7619/03_2024/6cu8_7619.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cu8_7619/03_2024/6cu8_7619.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cu8_7619/03_2024/6cu8_7619.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2880 Number of models: 1 Model: "" Number of chains: 10 Chain: "E" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 288 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "A" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 288 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "B" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 288 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "C" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 288 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "D" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 288 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "F" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 288 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "G" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 288 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "H" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 288 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "I" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 288 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "J" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 288 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Time building chain proxies: 1.57, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 0.94 Conformation dependent library (CDL) restraints added in 564.1 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: 0.30 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: 0.53 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 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: 104.74 - 110.02: 625 110.02 - 115.30: 1475 115.30 - 120.58: 757 120.58 - 125.86: 1033 125.86 - 131.14: 10 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 2.520 nonbonded pdb=" N ASN J 65 " pdb=" OD1 ASN J 65 " model vdw 2.412 2.520 nonbonded pdb=" N ASN H 65 " pdb=" OD1 ASN H 65 " model vdw 2.412 2.520 nonbonded pdb=" N ASN C 65 " pdb=" OD1 ASN C 65 " model vdw 2.412 2.520 nonbonded pdb=" N ASN F 65 " pdb=" OD1 ASN F 65 " model vdw 2.412 2.520 ... (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 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: 0.290 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: 1.660 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.530 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.540 ------------------------------------------------------------------------------- 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 : 0.346 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: 0.1165 time to fit residues: 15.9316 Evaluate side-chains 69 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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: 8.9990 chunk 30 optimal weight: 8.9990 chunk 16 optimal weight: 40.0000 chunk 10 optimal weight: 0.1980 chunk 20 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 12 optimal weight: 40.0000 chunk 19 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 overall best weight: 5.6388 ------------------------------------------------------------------------------- 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 H 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2880 Z= 0.238 Angle : 0.682 3.526 3900 Z= 0.406 Chirality : 0.054 0.119 540 Planarity : 0.003 0.013 480 Dihedral : 6.922 16.633 400 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 1.61 % Allowed : 13.87 % Favored : 84.52 % 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: -2.72 (0.44), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.34), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 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 : 0.343 Fit side-chains REVERT: A 58 LYS cc_start: 0.8411 (mttp) cc_final: 0.7533 (pttm) REVERT: A 61 GLU cc_start: 0.7648 (pm20) cc_final: 0.5993 (mm-30) REVERT: A 79 GLN cc_start: 0.8657 (tt0) cc_final: 0.8290 (tt0) REVERT: B 61 GLU cc_start: 0.7056 (pt0) cc_final: 0.6003 (mm-30) outliers start: 5 outliers final: 3 residues processed: 72 average time/residue: 0.0924 time to fit residues: 8.8109 Evaluate side-chains 57 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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: 10.0000 chunk 24 optimal weight: 20.0000 chunk 10 optimal weight: 0.0000 chunk 36 optimal weight: 3.9990 chunk 39 optimal weight: 20.0000 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 30.0000 chunk 29 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 overall best weight: 4.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 GLN B 79 GLN F 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.3951 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= 0.180 Angle : 0.608 3.465 3900 Z= 0.361 Chirality : 0.054 0.121 540 Planarity : 0.003 0.014 480 Dihedral : 6.362 13.491 400 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.58 % Allowed : 15.81 % Favored : 81.61 % 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: -2.37 (0.44), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.34), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 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 69 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 0.349 Fit side-chains REVERT: A 58 LYS cc_start: 0.8210 (mttp) cc_final: 0.7764 (pttp) REVERT: A 61 GLU cc_start: 0.7716 (pm20) cc_final: 0.5942 (mm-30) REVERT: B 61 GLU cc_start: 0.6776 (pt0) cc_final: 0.5841 (mm-30) outliers start: 8 outliers final: 5 residues processed: 69 average time/residue: 0.0791 time to fit residues: 7.5634 Evaluate side-chains 60 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain J 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: 0.3980 chunk 24 optimal weight: 30.0000 chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 19 optimal weight: 30.0000 chunk 34 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 overall best weight: 4.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2880 Z= 0.191 Angle : 0.593 3.473 3900 Z= 0.353 Chirality : 0.054 0.119 540 Planarity : 0.002 0.013 480 Dihedral : 6.164 13.384 400 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 2.58 % Allowed : 16.13 % Favored : 81.29 % 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: -2.23 (0.44), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.34), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 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 56 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.334 Fit side-chains REVERT: A 58 LYS cc_start: 0.8356 (mttp) cc_final: 0.7819 (pttp) REVERT: A 61 GLU cc_start: 0.7811 (pm20) cc_final: 0.5890 (mm-30) REVERT: B 61 GLU cc_start: 0.6853 (pt0) cc_final: 0.5947 (mm-30) outliers start: 8 outliers final: 5 residues processed: 56 average time/residue: 0.0786 time to fit residues: 6.1590 Evaluate side-chains 50 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 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: 40.0000 chunk 15 optimal weight: 30.0000 chunk 32 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 19 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 13 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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: 0.7456 moved from start: 0.4769 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= 0.282 Angle : 0.652 3.401 3900 Z= 0.389 Chirality : 0.055 0.123 540 Planarity : 0.003 0.013 480 Dihedral : 6.782 16.544 400 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 3.23 % Allowed : 15.48 % Favored : 81.29 % 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: -2.52 (0.41), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 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 55 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 45 time to evaluate : 0.351 Fit side-chains REVERT: A 61 GLU cc_start: 0.7821 (pm20) cc_final: 0.5870 (mm-30) REVERT: B 61 GLU cc_start: 0.7065 (pt0) cc_final: 0.6091 (mm-30) outliers start: 10 outliers final: 7 residues processed: 54 average time/residue: 0.0912 time to fit residues: 6.7400 Evaluate side-chains 46 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 3 optimal weight: 30.0000 chunk 12 optimal weight: 30.0000 chunk 20 optimal weight: 30.0000 chunk 37 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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: 0.7451 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2880 Z= 0.262 Angle : 0.637 4.913 3900 Z= 0.377 Chirality : 0.055 0.126 540 Planarity : 0.003 0.011 480 Dihedral : 6.595 15.193 400 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 3.87 % Allowed : 15.81 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.41), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.31), 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 57 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 45 time to evaluate : 0.348 Fit side-chains REVERT: A 61 GLU cc_start: 0.7786 (pm20) cc_final: 0.5902 (mm-30) REVERT: B 57 GLU cc_start: 0.3879 (OUTLIER) cc_final: 0.3056 (pp20) REVERT: B 61 GLU cc_start: 0.7212 (pt0) cc_final: 0.6112 (mm-30) REVERT: J 46 GLU cc_start: 0.6363 (tt0) cc_final: 0.5975 (tt0) outliers start: 12 outliers final: 8 residues processed: 54 average time/residue: 0.0863 time to fit residues: 6.4961 Evaluate side-chains 53 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 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 B residue 54 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain F residue 75 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: 1.9990 chunk 38 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 15 optimal weight: 30.0000 chunk 11 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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: 0.7434 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2880 Z= 0.225 Angle : 0.612 5.841 3900 Z= 0.361 Chirality : 0.055 0.125 540 Planarity : 0.002 0.011 480 Dihedral : 6.365 14.920 400 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 3.55 % Allowed : 16.45 % Favored : 80.00 % 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: -2.53 (0.41), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 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 58 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 47 time to evaluate : 0.342 Fit side-chains REVERT: A 61 GLU cc_start: 0.7787 (pm20) cc_final: 0.5831 (mm-30) REVERT: B 57 GLU cc_start: 0.3876 (OUTLIER) cc_final: 0.3040 (pp20) REVERT: B 61 GLU cc_start: 0.7136 (pt0) cc_final: 0.6130 (mm-30) outliers start: 11 outliers final: 8 residues processed: 54 average time/residue: 0.0822 time to fit residues: 6.1673 Evaluate side-chains 54 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 B residue 54 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 40.0000 chunk 30 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 11 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 overall best weight: 6.1788 ------------------------------------------------------------------------------- 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: 0.7453 moved from start: 0.5341 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= 0.254 Angle : 0.620 4.679 3900 Z= 0.367 Chirality : 0.055 0.125 540 Planarity : 0.002 0.011 480 Dihedral : 6.494 15.463 400 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % 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: -2.70 (0.40), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 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 56 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 44 time to evaluate : 0.346 Fit side-chains REVERT: A 61 GLU cc_start: 0.7809 (pm20) cc_final: 0.5833 (mm-30) REVERT: B 57 GLU cc_start: 0.4091 (OUTLIER) cc_final: 0.3217 (pt0) REVERT: B 61 GLU cc_start: 0.7208 (pt0) cc_final: 0.6145 (mm-30) outliers start: 12 outliers final: 10 residues processed: 51 average time/residue: 0.0985 time to fit residues: 6.6768 Evaluate side-chains 53 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 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 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: 7.9990 chunk 23 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 chunk 31 optimal weight: 9.9990 chunk 3 optimal weight: 30.0000 chunk 24 optimal weight: 20.0000 chunk 19 optimal weight: 6.9990 chunk 25 optimal weight: 20.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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: 0.7495 moved from start: 0.5556 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= 0.316 Angle : 0.660 4.068 3900 Z= 0.392 Chirality : 0.056 0.126 540 Planarity : 0.003 0.012 480 Dihedral : 6.872 16.045 400 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.85 % Favored : 86.15 % Rotamer: Outliers : 4.19 % Allowed : 16.13 % 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: -3.01 (0.39), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 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 56 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 43 time to evaluate : 0.329 Fit side-chains REVERT: A 61 GLU cc_start: 0.7822 (pm20) cc_final: 0.5855 (mm-30) REVERT: B 57 GLU cc_start: 0.4167 (OUTLIER) cc_final: 0.3192 (pt0) REVERT: B 61 GLU cc_start: 0.7268 (pt0) cc_final: 0.6174 (mm-30) outliers start: 13 outliers final: 11 residues processed: 51 average time/residue: 0.0714 time to fit residues: 5.2914 Evaluate side-chains 55 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 43 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 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 D residue 81 THR Chi-restraints excluded: chain F residue 54 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: 1.9990 chunk 29 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 31 optimal weight: 30.0000 chunk 13 optimal weight: 20.0000 chunk 32 optimal weight: 30.0000 chunk 5 optimal weight: 0.0470 chunk 27 optimal weight: 30.0000 chunk 1 optimal weight: 6.9990 overall best weight: 5.0086 ------------------------------------------------------------------------------- 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: 0.7438 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 0.023 2880 Z= 0.213 Angle : 0.587 4.000 3900 Z= 0.347 Chirality : 0.055 0.127 540 Planarity : 0.002 0.011 480 Dihedral : 6.359 15.230 400 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % 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: -2.70 (0.41), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 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 58 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 46 time to evaluate : 0.338 Fit side-chains REVERT: A 61 GLU cc_start: 0.7892 (pm20) cc_final: 0.5952 (mm-30) REVERT: B 57 GLU cc_start: 0.4056 (OUTLIER) cc_final: 0.3239 (pt0) REVERT: B 61 GLU cc_start: 0.7170 (pt0) cc_final: 0.6153 (mm-30) outliers start: 12 outliers final: 11 residues processed: 53 average time/residue: 0.0785 time to fit residues: 5.8858 Evaluate side-chains 56 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 44 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 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 D residue 81 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain J residue 45 LYS 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: 2.9990 chunk 36 optimal weight: 40.0000 chunk 21 optimal weight: 8.9990 chunk 27 optimal weight: 30.0000 chunk 1 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 23 optimal weight: 30.0000 chunk 15 optimal weight: 30.0000 chunk 14 optimal weight: 8.9990 chunk 39 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.116014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.102189 restraints weight = 7201.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.104631 restraints weight = 3611.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.106205 restraints weight = 2278.424| |-----------------------------------------------------------------------------| r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.5693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2880 Z= 0.285 Angle : 0.629 3.870 3900 Z= 0.374 Chirality : 0.056 0.125 540 Planarity : 0.003 0.012 480 Dihedral : 6.655 15.694 400 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.87 % Favored : 85.13 % Rotamer: Outliers : 3.87 % Allowed : 17.42 % Favored : 78.71 % 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: -2.94 (0.40), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 50 =============================================================================== Job complete usr+sys time: 798.09 seconds wall clock time: 15 minutes 23.26 seconds (923.26 seconds total)